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- PDB-6vk4: Crystal Structure of Methylosinus trichosporium OB3b Soluble Meth... -

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Basic information

Entry
Database: PDB / ID: 6vk4
TitleCrystal Structure of Methylosinus trichosporium OB3b Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex
Components
  • (Methane monooxygenase ...) x 2
  • (Methane monooxygenase) x 2
KeywordsOXIDOREDUCTASE / Methane Monooxygenase Hydroxylase
Function / homology
Function and homology information


methane metabolic process / methane monooxygenase (soluble) / methane monooxygenase [NAD(P)H] activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / one-carbon metabolic process / monooxygenase activity / metal ion binding
Similarity search - Function
: / Monooxygenase component MmoB/DmpM / Monooxygenase component MmoB/DmpM superfamily / MmoB/DmpM family / : / : / Methane monooxygenase, gamma chain / Methane monooxygenase, gamma chain, domain 1 / Methane monooxygenase, gamma chain, domain 2 / Methane monooxygenase, gamma chain superfamily ...: / Monooxygenase component MmoB/DmpM / Monooxygenase component MmoB/DmpM superfamily / MmoB/DmpM family / : / : / Methane monooxygenase, gamma chain / Methane monooxygenase, gamma chain, domain 1 / Methane monooxygenase, gamma chain, domain 2 / Methane monooxygenase, gamma chain superfamily / Methane monooxygenase, hydrolase gamma chain / Methane/phenol monooxygenase, hydroxylase component / Propane/methane/phenol/toluene hydroxylase / Methane/Phenol/Alkene Hydroxylase / Ribonucleotide reductase-like / Ferritin-like superfamily
Similarity search - Domain/homology
BENZOIC ACID / : / : / Methane monooxygenase / Methane monooxygenase regulatory protein B / Methane monooxygenase component A alpha chain / Methane monooxygenase / Methane monooxygenase component A alpha chain / Methane monooxygenase regulatory protein B
Similarity search - Component
Biological speciesMethylosinus trichosporium OB3b (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.35 Å
AuthorsJones, J.C. / Banerjee, R. / Shi, K. / Aihara, H. / Lipscomb, J.D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118030, GM08347 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118000, GM118047 United States
CitationJournal: Biochemistry / Year: 2020
Title: Structural Studies of theMethylosinus trichosporiumOB3b Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex Reveal a Transient Substrate Tunnel.
Authors: Jones, J.C. / Banerjee, R. / Shi, K. / Aihara, H. / Lipscomb, J.D.
History
DepositionJan 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Nov 17, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / cell / database_2 / entity / pdbx_contact_author / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_site / struct_site_gen
Item: _cell.volume / _database_2.pdbx_DOI ..._cell.volume / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_entry_details.has_ligand_of_interest / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_validate_torsion.auth_asym_id / _pdbx_validate_torsion.auth_comp_id / _pdbx_validate_torsion.auth_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _reflns.B_iso_Wilson_estimate / _reflns.number_obs / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Polymer geometry / Details: An unfit sidechain / Provider: author / Type: Coordinate replacement
Revision 2.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methane monooxygenase component A alpha chain
B: Methane monooxygenase
C: Methane monooxygenase
D: Methane monooxygenase regulatory protein B
E: Methane monooxygenase component A alpha chain
F: Methane monooxygenase
G: Methane monooxygenase
H: Methane monooxygenase regulatory protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)279,86615
Polymers279,3368
Non-polymers5307
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58340 Å2
ΔGint-224 kcal/mol
Surface area64500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.861, 105.207, 300.877
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Methane monooxygenase ... , 2 types, 4 molecules AEDH

#1: Protein Methane monooxygenase component A alpha chain


Mass: 60031.293 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Methylosinus trichosporium OB3b (bacteria)
References: UniProt: A0A2D2D5X0, UniProt: P27353*PLUS
#4: Protein Methane monooxygenase regulatory protein B


Mass: 14896.885 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Methylosinus trichosporium OB3b (bacteria)
References: UniProt: A0A2D2D0T8, UniProt: P27356*PLUS

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Protein , 2 types, 4 molecules BFCG

#2: Protein Methane monooxygenase


Mass: 45295.340 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Methylosinus trichosporium OB3b (bacteria)
References: UniProt: A0A2D2D5X7
#3: Protein Methane monooxygenase


Mass: 19444.400 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Methylosinus trichosporium OB3b (bacteria)
References: UniProt: A0A2D2D0T0

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Non-polymers , 5 types, 302 molecules

#5: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#6: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#8: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Tacsimate and PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.35→102.86 Å / Num. obs: 131580 / % possible obs: 98.4 % / Redundancy: 4.3 % / Biso Wilson estimate: 56.99 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.147 / Net I/σ(I): 5.7
Reflection shellResolution: 2.35→2.39 Å / Num. unique obs: 6698 / CC1/2: 0.287 / Rpim(I) all: 1.332

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Processing

Software
NameVersionClassification
PHENIX1.20rc2_4400refinement
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.35→52.59 Å / SU ML: 0.4237 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.7665
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2278 6689 5.09 %
Rwork0.19 124787 -
obs0.1919 131476 96.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.9 Å2
Refinement stepCycle: LAST / Resolution: 2.35→52.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19389 0 26 295 19710
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004919940
X-RAY DIFFRACTIONf_angle_d0.689627070
X-RAY DIFFRACTIONf_chiral_restr0.04452840
X-RAY DIFFRACTIONf_plane_restr0.00593495
X-RAY DIFFRACTIONf_dihedral_angle_d16.99077150
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.380.43811610.39753405X-RAY DIFFRACTION78.65
2.38-2.40.39432090.38693755X-RAY DIFFRACTION88.54
2.4-2.430.44722270.36543960X-RAY DIFFRACTION93.29
2.43-2.460.39092440.36143999X-RAY DIFFRACTION93.71
2.46-2.50.39472270.3574111X-RAY DIFFRACTION96.08
2.5-2.530.36482520.33084068X-RAY DIFFRACTION96.97
2.53-2.570.35172120.31544286X-RAY DIFFRACTION98.66
2.57-2.610.30972240.30284193X-RAY DIFFRACTION99.46
2.61-2.650.35522050.30374282X-RAY DIFFRACTION99.25
2.65-2.690.32412490.29634262X-RAY DIFFRACTION99.49
2.69-2.740.33442250.2924216X-RAY DIFFRACTION99.42
2.74-2.790.33132400.28924298X-RAY DIFFRACTION99.08
2.79-2.840.37382470.29714205X-RAY DIFFRACTION99.07
2.84-2.90.34152190.30074233X-RAY DIFFRACTION99.02
2.9-2.960.34482040.27634263X-RAY DIFFRACTION98.48
2.96-3.030.31542070.25354263X-RAY DIFFRACTION98.81
3.03-3.110.2912070.24634258X-RAY DIFFRACTION98.54
3.11-3.190.28852290.22994247X-RAY DIFFRACTION98.35
3.19-3.280.30191960.23244256X-RAY DIFFRACTION98.26
3.28-3.390.25482200.22354198X-RAY DIFFRACTION97.42
3.39-3.510.23222290.20024153X-RAY DIFFRACTION96.31
3.51-3.650.22912280.1734098X-RAY DIFFRACTION95.39
3.65-3.820.19152290.164204X-RAY DIFFRACTION97.13
3.82-4.020.18262260.15044223X-RAY DIFFRACTION97.44
4.02-4.270.18061970.13724256X-RAY DIFFRACTION97.04
4.27-4.60.17262280.13034224X-RAY DIFFRACTION96.59
4.6-5.060.17472190.13024219X-RAY DIFFRACTION96.44
5.06-5.790.17152330.13914242X-RAY DIFFRACTION96.3
5.79-7.290.1942320.14214133X-RAY DIFFRACTION93.17
7.3-52.590.14642640.13394277X-RAY DIFFRACTION92.67
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.04283437817-0.78298466384-1.330716388453.965329308013.271231346917.665613505770.05588115093210.3154029870810.0719325732273-0.274346670897-0.250214555710.525467153115-0.252758262125-0.9695960336850.2671700042890.4882505060820.0592455973149-0.04720752008070.8074539015310.07635368910140.580434723828-31.163539602623.346165337337.5529064634
20.8656945169820.814521514109-0.2131216737871.10055051123-0.004338055480811.766886699610.07624818723480.1746633351220.0115866799615-0.0479642031508-0.01952440770370.126476637363-0.0205109073523-0.36116134817-0.04867425468440.5369100239510.1226224840620.02198366737850.4983359738050.03056823163660.474250944855-9.3699642937436.694146809348.5810994427
30.229787803253-0.528522817277-0.1209796948380.9772496880270.3993121321080.8801060718180.02159387998410.115077809111-0.0480820296654-0.013293015182-0.04025872437160.11983745305-0.144676417312-0.1784821119890.02331054090940.6425376021770.07022014342660.07058641941940.5795432004990.02661904302280.563372934909-9.1330441716644.997950592251.9330960227
41.291744485920.811843230632-0.5712906831360.736478520288-0.03229454611871.222517101840.0296995850970.1833054896370.190994886661-0.124146577055-0.01166689639740.327816759561-0.270143492948-0.372304410525-0.0285028453150.6583768986470.2151173086490.03306085244910.5494857513050.02744254771140.587126723131-12.964306296457.418488486149.5133143564
51.32124483630.5291619276411.177769825481.848036912720.159617842432.158255016720.0126248017511-0.07585555683980.328035919157-0.0960781208130.0684095684468-0.111021430946-0.356319536727-0.0336398215563-0.07525176546750.6465652608120.0806963613620.07938492106520.4179236280390.01503099917020.4842864580413.5940728639461.309679474757.2454757298
61.254962734140.1036424277330.3203273611881.113534586690.2232782815830.8070068928280.00717187766509-0.2187253866720.1399163527380.1476838608320.007878748458130.136882002047-0.217144204294-0.0816172524371-0.01516554435810.6776843486740.07912292060710.09017357704790.464170183851-0.01484799953290.4702877964920.81564347994356.456571412271.6183896143
73.586996036350.528664622971-0.2768385714523.72046374031-2.47907785649.07189413277-0.04520166378460.414769192052-0.07171843605390.03686090344610.06028829455970.0487904303038-0.6641310978640.38706114583-0.02039264886640.4681327035050.02152952434640.05592962839190.401484585864-0.1265408259970.4513632930814.604729908547.23137101945.4271701207
80.8085341558480.1285797202970.03114523290650.6356768124770.05180464600210.6813768292630.04366776285050.08786148347920.02954202435750.144635874579-0.02192719190440.1825629449680.0547339482472-0.214611532023-0.01234492857080.4865521991830.01942972145140.04684428764550.5378353536650.02431030936420.510783672452-20.982164436120.444204003752.5756744669
92.228792755781.621660677621.979247345173.11400504082.419158441393.499308993280.186396653586-0.162334486056-0.05782589740360.422258957011-0.2463358984530.3116399214590.500299526139-0.5863263880150.04724999254320.583166488855-0.06977439047730.1052575407710.6163269723060.04930361634960.575282516604-31.69451093015.3783351759360.5386213349
108.533366623654.524583399553.389114951223.261027439844.360904876859.194604953960.74856581079-1.37118842747-0.1799236562990.296030950216-0.732001474742-0.142084080323-0.628481114749-0.3391827295670.01099530135410.79771288965-0.06495337856570.1159042719670.6521775023250.02923831984860.580356887892-2.544526026942.970141433984.7606641805
117.587723124767.37386487636-1.232119643399.38276735177-1.349451639321.146114907660.935148296065-0.823699531174-0.294873208841.38916053269-0.5945845909960.230142566302-0.294733605114-0.294964705186-0.3482760309760.9093245182420.02668527410790.06088079610780.6657034693450.05885016215160.511087280303-14.047793500633.725888666391.2622526251
121.611419099370.1514918575021.531953710032.033774355260.8194877446611.689919458840.229433100781-0.7552141966080.2498299827951.23549491456-0.0474427347751.19198320205-0.306627704021-0.308931326815-0.1634012139140.7812743001420.1519711160130.258259742610.649905592347-0.05451286438790.691025462891-24.994956198137.020949895788.1270682894
138.86292623442-4.824747760913.262091549537.74126582237-3.829868540312.040550532890.113577687914-0.3451261608670.927989390507-0.247973034832-0.270394998652-0.2537982024780.0283318230701-0.1245750662360.1552211905360.8723935456060.05437934594950.150758524620.549436954805-0.04645003788780.684201950809-17.964523041848.361744743583.7392549714
141.013098498430.56766088397-0.08302499071111.632206692541.349597120142.254459220110.198243081429-0.1858200290920.0888537633347-0.0373217896756-0.1636098385350.114416452625-0.0532230296845-0.070032864597-0.02731916935770.6898791085030.06754815798690.1410720929090.5696814804540.007082211498780.570810491362-23.139768062127.967710704882.0907966198
152.77750805236-4.47838855898-0.7416693087847.238485719621.633837275159.711178540250.152530825803-0.538617267887-0.6321343445340.818979200351-0.3214966920031.17658442226-0.454014625923-0.9577257269640.1657064153590.77380781302-0.05142429809050.237382236010.817438954928-0.02373726377790.748015301107-36.770066993330.096796825282.4636443955
160.6752254261310.7471265290610.1374983427961.49974254425-0.3977276326490.4182951781450.0530463937771-0.109810459280.2309013717750.350846467739-0.07532550347580.4259028283560.0542674622356-0.3051380031430.05988112616180.603362194880.1051536398590.168861090770.856189580162-0.04622972140330.698365955425-34.59499412143.560749114776.0477745123
171.49825150459-1.6072569982-0.09834380693077.07763368978-0.6466920833371.51087101604-0.1789908432680.250041636051-0.2617242991620.3904747426090.3951834331510.912153867805-0.25232735348-0.82823581731-0.207747196330.4431661350550.1640789044180.1208077272840.6698363766970.02969175399220.735258680629-32.762902909442.057061412468.1556421021
187.734981231414.48361476511-0.2641295914632.740612025370.3592542262312.60361479761-0.505322701972-0.232602851660.502531572140.1682133806570.3690517839440.716484182819-0.579918374748-0.9221893472950.1249259350120.6777431337540.2322748502710.0235374685570.7765141673410.04183636653690.832103209784-29.770727407661.937336688463.1736891681
195.13475504651-4.0123657751-3.508130978954.306523246314.788238706275.97124764546-0.115642685224-0.06122518343490.770742562921-0.1626171235740.1318088421190.195306845754-0.765568057274-0.577638293676-0.020333855320.7364073884650.2026799552190.09105090892370.6150361712190.02707086419880.87297606329-25.982573704865.848911826373.2022495349
204.7323157801-0.864928313602-0.8075945129072.095021763850.4469981313811.220551935580.5483321108850.36398217618-0.496812739119-0.321871466448-0.340238903017-0.51897215878-0.02928694127660.0450839200745-0.2020776368160.6694314515460.2133614608420.04697625240040.529473438791-0.1363449483630.731941299332-16.158753260867.890046852577.6507119361
214.221787698113.050448661380.4413194709599.220621321953.100395622821.71221041609-0.09090884223120.6580816902010.7156311608880.03652825363280.2248151600420.913231818233-0.679554984242-0.0647640529138-0.08212278689210.8548863129280.198434227051-0.0117014432070.6085425901980.1417549742220.664438433392-4.5529080784167.469224096538.8844462364
228.879509579321.597199087677.200684378372.2336415073-0.6072487200287.89595464878-1.027366008220.2061389399231.42264556081-0.6885143055540.3402696248170.665715915708-1.3098424367-0.2609031467910.6454060805220.9358368333880.153997767873-0.05543165262960.6419278285540.1198801263420.782211849842-16.195089713268.197871772943.2686383815
236.54219422679-4.363579805864.381532333957.7630275588-2.60322994252.955871614860.2555737194220.799289571316-0.296423433087-0.732726240004-0.0552999089966-0.07459950721720.574650231650.234464751749-0.2202105473250.6860561561120.03030396212480.02163620821230.71522385274-0.003732824174240.579944473307-4.6674246872443.879319895229.3192706955
242.64714520144-0.706906415222-0.6569627138293.580134164792.52105930511.79883863037-0.05885668179850.410003063007-0.155072752576-0.345322810455-0.05179704920970.221120827334-0.154114473404-0.2642404669820.1097520566410.771338282090.1277141412940.05290638217060.7547884961070.07576301861810.59901572137-11.167338710744.467489596528.4336124833
257.126672644785.97866392099-4.834076615498.57544837034-0.1460963351599.114982645910.1875275187921.440004910710.803529954779-0.981975338445-0.04226066386021.67658579401-0.887473357488-1.82596761628-0.1090952529760.9928003318890.204485509913-0.01581161570511.238823488220.09177883453591.02444372515-27.858111298351.871030769634.9989057254
263.32748357599-0.457067846039-3.086330837340.2811563713911.043631916584.46303874616-0.21822361667-0.171300771673-0.362078659483-0.0668260318240.00981364481488-0.0673127597570.4082701869130.3129522417140.2193553434520.8335436447840.111932013353-0.02604721822520.5492106520050.04408942471760.5776550988544.38913155973-4.6279699240434.2178101213
270.839885300560.472224292348-0.009013620561850.3428198046690.03320752768781.19345894288-0.05479996248050.137565242914-0.126859273152-0.06383458886820.0926414803819-0.02008453794580.15144640418-0.138198303939-0.004355565580610.5663160043870.0849185754696-0.001757460479390.620996720765-0.02564708541590.53346323500210.272575732720.732227225226.3366568856
280.837155768364-0.00349742563362-0.01906904113270.241099522392-0.08498661934081.07605875355-0.009378981213650.0971220702647-0.164038156460.122202005534-0.0681859076035-0.05695200260210.2808228637840.1672011938770.05428114238450.5945301478950.0826161473026-0.002109976827710.655572849529-0.04081807810220.55731631004519.383237842217.259200012323.261880612
290.482535382630.12418826429-0.000866047463710.7415306432380.1558765564320.9139674042160.000190111728814-0.123842546675-0.2261363646290.06048306649940.0637529900921-0.04919936125480.1494162969490.3224833445220.00540380174290.574352027010.1426507217850.001490316246830.775573502111-0.01516773468930.59702327896331.261748661516.269581845224.7677411673
300.8142804007840.462754534215-0.6484053874261.527926999510.02893283103931.815085184470.0314245866428-0.0280122249255-0.14624495284-0.094102078885-0.288124883581-0.3661226202260.4071095049780.7148090205730.290233885660.5413172827540.191139019891-0.009250797497490.808522966581-0.08412412615560.54426397164236.731717503315.466538335522.4348337849
310.8972589380040.0291954522202-0.1405694300541.33240404033-0.166172689972.333365210710.07418700238320.03436969389670.179843710897-0.1247898914890.00252206459013-0.182768039375-0.2302982003020.481900371424-0.08922767372060.5317558449140.02993124697450.02593527535170.681683104701-0.03397881816780.51761278154334.961911919738.261186090613.9202423693
320.4896658556510.312440971033-0.4967640178361.083736661220.2950107680721.0141625398-0.02692501764650.154691884956-0.0545923780715-0.3229202429720.0726172173652-0.0999310920036-0.05911680209490.133438614473-0.04312635544930.5959027600590.08329386371520.03948259563960.749470860533-0.0397682031290.48235732034429.256212569924.69058447092.35228938966
335.200019529181.016706144063.114902502583.206905718212.46866025817.56502201967-0.181881921004-0.2059763654990.06266164965680.3231970229170.257380408042-0.0736360374847-0.5981247652580.412346491543-0.05981017508630.4756460416280.00609007993250.1460076357670.471147436027-0.002541682782160.40853472857620.835795779641.074957346629.8513187935
340.6137702763810.103994525389-0.1405657066520.5325180125730.1798134334630.936521814857-0.04049056973520.224858934904-0.110375100756-0.06942093126840.02650224683090.03325694339680.212903928129-0.1676055812980.02007908326290.5705149828340.0224819390612-0.03132295669230.591864338529-0.05526510236290.508763925476-5.486432608453.5761099547821.4623223907
353.638118127372.57203017295-2.552849815414.70468328429-2.290590000411.86110825848-0.1276136253330.612704865654-0.0265394987282-0.3771416113050.3106700594160.3363484830250.326131530509-0.776548235733-0.15489922330.590257995956-0.119453800105-0.06203788451540.784570242914-0.07051046405870.534068970835-23.8402740959-6.4431783913116.7934911561
364.354335951214.52245627495-4.399375366838.23561789598-2.979543285275.15840253442-0.9619418682061.06801013025-0.0758069584007-1.288599386610.8872557878590.02198594783020.4636951095560.1088901361530.08237527843280.902888981568-0.03766381745230.01391913464710.854603723554-0.02663494864360.50600095561217.290172966723.7351755993-9.60512601257
374.427405012386.160231897451.685307787928.63749622622.222493564780.974261763214-0.4145153422081.0439380304-0.0396530602868-0.9902834782820.5252666388570.462252364238-0.0460697413529-0.227292854554-0.1159765468580.8829569166640.116230425219-0.06269173090090.94010600095-0.03985744364790.6340923494798.379363089611.8555576016-16.0924004014
382.613249437383.27652576088-2.752661976295.42946536356-3.460787278122.90110365634-0.5194990426550.280110188858-0.260054157877-1.244174530660.326051519689-0.01616507802810.5352337035780.2351104819430.1781401363190.821364329940.1119908892030.06832554857720.803796170182-0.1232075279970.51971396841412.00563477090.97452127808-12.9239285169
392.01695905444-3.90954999844-0.3539598578489.388959766651.898539808659.10661352225-0.1992012838231.09470218937-0.0847948731034-1.13216168735-0.222286947328-0.3978521164840.4325094674260.1564898409320.4011428863330.6944472592410.05595501724760.03696923235610.838423246009-0.02353200596030.61277411789224.03915235166.45835432058-8.88525101301
405.203889550764.43201017646-1.97763735975.7797810359-0.9334319523331.33775646841-0.6175387823210.880262365216-0.351615235264-0.5651105573620.665308253199-0.2063613653180.19363832069-0.190419712372-0.045690814310.707803952950.0598561269513-0.001777379644640.798062495064-0.112537604030.5114226015474.538988434573.81378545721-6.91837676905
417.63643167795-4.18456794182-3.048634719985.792061869851.137966276258.91528955803-0.6720296354290.748567080365-0.9358507625250.03596112072270.3179062325320.09592630122240.618859210896-0.3158163377510.3852059093320.9526301263510.00819071035483-0.07130136967510.816695754535-0.2412417091050.7473092763165.38028017982-10.9332259794-7.18317359095
425.937645530715.028437665723.873973671585.20774460231.967084237194.439492784760.3096912315680.830397015337-0.989067325012-0.417745791791-0.27157916724-0.3656479115020.2511857437950.185213598163-0.08203765219470.8605617215480.04220247068680.1105541630020.610098430771-0.10637923010.74791219305118.6584542993-13.98483417971.024100135
433.53073181938-0.188044618971.568569402650.311024553189-0.4299883418651.080647604120.0866840599705-0.2546957687680.14856623804-0.308761977825-0.0760193292393-0.0323152057980.337821599573-0.193195362617-0.01890189526370.772045920280.1224440742080.06960791455170.806418826531-0.1184710105340.61454384509818.8537003431-4.72111434609-1.92426460437
441.97349725599-1.29550332090.7503853620292.939841192470.1919675470673.611158142740.001677231696680.191779769887-0.983755862674-0.01759821093870.21345084666-0.1661224898630.9694610625210.258493395751-0.158848834170.6509946316680.07640976952370.08399063949380.516566430841-0.1027536878940.5696693197517.1692553977-6.565348448027.12507792722
459.198329039374.17892843723-2.640858128971.9505729061-1.108787770350.9114221363030.0615732100676-0.965649359953-0.601529609873-0.250366406856-0.148010761553-0.8157499390870.9455857379650.9346859489530.1033298769920.6661979176360.224376454714-0.01221718053430.8309352286720.05182715613020.73454861900536.9022874295-3.0268331362812.1166712476
464.80183172539-4.46918407667-6.023986128524.213998659825.680310445517.687080010560.6427215605350.640977311255-0.3575503599420.3597296051330.670186181645-1.724763485210.1205856554850.434660476086-1.313442824240.8265040172820.2131232075340.01321971984280.703063425943-0.07472881699790.79108211542640.81789883570.9137411407492.14859025608
472.09198047151-3.82951203854-2.692103213177.952836686174.08891582696.38187360671-0.253481706553-0.3483410409050.0931897028825-0.2764997561120.08324903085060.1622985761680.3170364121040.9584218249290.1119984261470.5773186727040.1362169658930.1284022126340.714302107478-0.02903889851690.74400072252142.571752445310.7330245907-2.16874565435
485.29751773731.620762522920.4243666201227.64587896769-1.661494321025.762086048920.322691048903-0.61251018992-0.4041051196331.009844446190.0655545159743-0.184545056488-0.523350467594-0.0104546939416-0.349698107780.753436047620.158356413996-0.0348589309471.015000712530.05574578400170.71010588065435.754948816220.178861810843.0739219123
492.278225571272.435774633190.5386978310447.07328785567-2.436600916532.213810512250.103912756831-0.0403317335562-0.3780019921570.0804305966056-0.162209977997-0.903268451666-0.2440933602670.317369607624-0.0286005881690.6425775264090.02018526200030.02361575340771.01862002392-0.06354343932360.74994036688644.891669950723.768525526432.6761442311
503.531098131772.97903201138-4.433483845419.17021004173-8.080667990219.31174725422-0.0171004437523-1.24912197387-0.7669917165640.150236013794-0.803337961812-1.08246479980.1280923414271.739349237930.7543645371480.6569345397480.170164963682-0.05143429122921.185007463150.09390510861390.69465242419742.654337625110.888610082432.0200758697
514.3357050571-4.23403640879-0.9608520887718.12845032481-1.273801473917.523019310270.0155789974-0.2684835932770.05815131179270.586388210208-0.0071505428580.220150271382-0.1942956598620.006156735362950.002806077735310.6244456358830.0504466979636-0.01506442183850.5497758711650.001301250949010.58966553447418.112993143821.746258347745.8873166221
527.10638287529-3.858114994374.80012560924.33158388565-4.55656478314.99467586411-0.594497247946-0.9745109573050.1336219640870.9080462519780.00261065558205-0.9232041635490.4080797863450.142534706480.6309768529570.9169258166820.182476086465-0.02312996534811.00696670920.04646793447670.69717826461923.729418734516.98041818355.0788911993
534.92638994059-0.170101260658-2.162437587526.453457565332.418715828451.79783211801-0.155042893968-0.7918549514480.2309560070610.9436897924480.193950123231-0.4314918305030.1953645162540.130109357280.03671110477430.6613661981390.0904342810151-0.04617524476670.809976257567-0.01870659214450.54348398453327.200324377920.514245269244.6770385381
546.87948743832-3.28406893442-6.348889205173.951145200923.717181692887.03012230202-0.467417448065-0.173315649766-0.530084997580.6554020477650.09522970775320.4067174403370.736956529154-0.02439105185260.3757402681990.6980903916520.03883813026520.004463010987080.633063886584-0.01699499013820.59120781210314.026782425112.438779806246.1758036352
550.3595222459621.060067035631.025951859016.445337338941.273097945984.087765669720.181060357612-0.04980428589880.1283751103540.0934258750603-0.2489802605420.1472587472430.293164177394-0.4412796864810.09771035974841.109021885290.335547311455-0.08076035954831.06091860926-0.09764345889340.94961557282426.7298984315-1.3640877810940.1996532273
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 12 through 45 )AA12 - 451 - 34
22chain 'A' and (resid 46 through 161 )AA46 - 16135 - 150
33chain 'A' and (resid 162 through 260 )AA162 - 260151 - 249
44chain 'A' and (resid 261 through 331 )AA261 - 331250 - 320
55chain 'A' and (resid 332 through 378 )AA332 - 378321 - 367
66chain 'A' and (resid 379 through 526 )AA379 - 526368 - 515
77chain 'B' and (resid 4 through 36 )BF4 - 361 - 33
88chain 'B' and (resid 37 through 312 )BF37 - 31234 - 309
99chain 'B' and (resid 313 through 394 )BF313 - 394310 - 391
1010chain 'C' and (resid 2 through 10 )CH2 - 101 - 9
1111chain 'C' and (resid 11 through 25 )CH11 - 2510 - 24
1212chain 'C' and (resid 26 through 40 )CH26 - 4025 - 39
1313chain 'C' and (resid 41 through 53 )CH41 - 5340 - 52
1414chain 'C' and (resid 54 through 80 )CH54 - 8053 - 79
1515chain 'C' and (resid 81 through 87 )CH81 - 8780 - 86
1616chain 'C' and (resid 88 through 125 )CH88 - 12587 - 124
1717chain 'C' and (resid 126 through 144 )CH126 - 144125 - 143
1818chain 'C' and (resid 145 through 152 )CH145 - 152144 - 151
1919chain 'C' and (resid 153 through 160 )CH153 - 160152 - 159
2020chain 'C' and (resid 161 through 168 )CH161 - 168160 - 167
2121chain 'D' and (resid 3 through 24 )DK3 - 241 - 22
2222chain 'D' and (resid 25 through 36 )DK25 - 3623 - 34
2323chain 'D' and (resid 37 through 54 )DK37 - 5435 - 52
2424chain 'D' and (resid 55 through 125 )DK55 - 12553 - 123
2525chain 'D' and (resid 126 through 132 )DK126 - 132124 - 130
2626chain 'E' and (resid 12 through 63 )EM12 - 631 - 52
2727chain 'E' and (resid 64 through 161 )EM64 - 16153 - 150
2828chain 'E' and (resid 162 through 260 )EM162 - 260151 - 249
2929chain 'E' and (resid 261 through 317 )EM261 - 317250 - 306
3030chain 'E' and (resid 318 through 352 )EM318 - 352307 - 341
3131chain 'E' and (resid 353 through 403 )EM353 - 403342 - 392
3232chain 'E' and (resid 404 through 526 )EM404 - 526393 - 515
3333chain 'F' and (resid 4 through 36 )FR4 - 361 - 33
3434chain 'F' and (resid 37 through 343 )FR37 - 34334 - 340
3535chain 'F' and (resid 344 through 394 )FR344 - 394341 - 391
3636chain 'G' and (resid 2 through 10 )GT2 - 101 - 9
3737chain 'G' and (resid 11 through 25 )GT11 - 2510 - 24
3838chain 'G' and (resid 26 through 40 )GT26 - 4025 - 39
3939chain 'G' and (resid 41 through 50 )GT41 - 5040 - 49
4040chain 'G' and (resid 51 through 80 )GT51 - 8050 - 79
4141chain 'G' and (resid 81 through 87 )GT81 - 8780 - 86
4242chain 'G' and (resid 88 through 104 )GT88 - 10487 - 103
4343chain 'G' and (resid 105 through 125 )GT105 - 125104 - 124
4444chain 'G' and (resid 126 through 144 )GT126 - 144125 - 143
4545chain 'G' and (resid 145 through 152 )GT145 - 152144 - 151
4646chain 'G' and (resid 153 through 160 )GT153 - 160152 - 159
4747chain 'G' and (resid 161 through 168 )GT161 - 168160 - 167
4848chain 'H' and (resid 3 through 10 )HV3 - 101 - 8
4949chain 'H' and (resid 11 through 24 )HV11 - 249 - 22
5050chain 'H' and (resid 25 through 36 )HV25 - 3623 - 34
5151chain 'H' and (resid 37 through 54 )HV37 - 5435 - 52
5252chain 'H' and (resid 55 through 63 )HV55 - 6353 - 61
5353chain 'H' and (resid 64 through 82 )HV64 - 8262 - 80
5454chain 'H' and (resid 83 through 125 )HV83 - 12581 - 123
5555chain 'H' and (resid 126 through 132 )HV126 - 132124 - 130

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About Yorodumi

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Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

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Related info.:EMDB header

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