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- PDB-4gam: Complex structure of Methane monooxygenase hydroxylase and regula... -

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Basic information

Entry
Database: PDB / ID: 4gam
TitleComplex structure of Methane monooxygenase hydroxylase and regulatory subunit
Components
  • (Methane monooxygenase component A ...) x 3
  • Methane monooxygenase regulatory protein B
KeywordsOXIDOREDUCTASE / Methane Monooxygenase / hydroxylase / regulatory subunit B
Function / homology
Function and homology information


methane metabolic process / methane monooxygenase (soluble) / : / : / : / monooxygenase activity / one-carbon metabolic process / metal ion binding
Similarity search - Function
Monooxygenase component MmoB/DmpM / Phenol Hydroxylase P2 Protein / Methane monooxygenase, gamma chain, domain 1 / Methane monooxygenase, gamma chain, domain 2 / 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 ...Monooxygenase component MmoB/DmpM / Phenol Hydroxylase P2 Protein / Methane monooxygenase, gamma chain, domain 1 / Methane monooxygenase, gamma chain, domain 2 / 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, subunit A / Ribonucleotide Reductase, subunit A / Monooxygenase / Ribonucleotide reductase-like / Ferritin-like superfamily / Alpha-Beta Complex / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Methane monooxygenase component A gamma chain / Methane monooxygenase regulatory protein B / Methane monooxygenase component A beta chain / Methane monooxygenase component A alpha chain
Similarity search - Component
Biological speciesMethylococcus capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.902 Å
AuthorsLee, S.J. / Lippard, S.J. / Cho, U.-S.
CitationJournal: Nature / Year: 2013
Title: Control of substrate access to the active site in methane monooxygenase.
Authors: Lee, S.J. / McCormick, M.S. / Lippard, S.J. / Cho, U.S.
History
DepositionJul 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Methane monooxygenase component A beta chain
A: Methane monooxygenase component A alpha chain
C: Methane monooxygenase component A gamma chain
D: Methane monooxygenase regulatory protein B
G: Methane monooxygenase component A beta chain
F: Methane monooxygenase component A alpha chain
H: Methane monooxygenase component A gamma chain
I: Methane monooxygenase regulatory protein B
L: Methane monooxygenase component A beta chain
K: Methane monooxygenase component A alpha chain
M: Methane monooxygenase component A gamma chain
N: Methane monooxygenase regulatory protein B
Q: Methane monooxygenase component A beta chain
P: Methane monooxygenase component A alpha chain
R: Methane monooxygenase component A gamma chain
S: Methane monooxygenase regulatory protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)567,57224
Polymers567,12616
Non-polymers4478
Water81145
1
B: Methane monooxygenase component A beta chain
A: Methane monooxygenase component A alpha chain
C: Methane monooxygenase component A gamma chain
D: Methane monooxygenase regulatory protein B
G: Methane monooxygenase component A beta chain
F: Methane monooxygenase component A alpha chain
H: Methane monooxygenase component A gamma chain
I: Methane monooxygenase regulatory protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)283,78612
Polymers283,5638
Non-polymers2234
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area54750 Å2
ΔGint-234 kcal/mol
Surface area66040 Å2
MethodPISA
2
L: Methane monooxygenase component A beta chain
K: Methane monooxygenase component A alpha chain
M: Methane monooxygenase component A gamma chain
N: Methane monooxygenase regulatory protein B
Q: Methane monooxygenase component A beta chain
P: Methane monooxygenase component A alpha chain
R: Methane monooxygenase component A gamma chain
S: Methane monooxygenase regulatory protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)283,78612
Polymers283,5638
Non-polymers2234
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area54910 Å2
ΔGint-247 kcal/mol
Surface area66610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.590, 248.970, 122.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Methane monooxygenase component A ... , 3 types, 12 molecules BGLQAFKPCHMR

#1: Protein
Methane monooxygenase component A beta chain / Methane hydroxylase


Mass: 45184.660 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: MMOH : Purified from the original bacteria / Source: (natural) Methylococcus capsulatus (bacteria) / Strain: Methylococcus capsulatus
References: UniProt: P18798, methane monooxygenase (soluble)
#2: Protein
Methane monooxygenase component A alpha chain / Methane hydroxylase


Mass: 60717.145 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: MMOH : Purified from the original bacteria / Source: (natural) Methylococcus capsulatus (bacteria) / Strain: Methylococcus capsulatus
References: UniProt: P22869, methane monooxygenase (soluble)
#3: Protein
Methane monooxygenase component A gamma chain / Methane hydroxylase


Mass: 19879.732 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: MMOH : Purified from the original bacteria / Source: (natural) Methylococcus capsulatus (bacteria) / Strain: Methylococcus capsulatus
References: UniProt: P11987, methane monooxygenase (soluble)

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Protein , 1 types, 4 molecules DINS

#4: Protein
Methane monooxygenase regulatory protein B


Mass: 15999.864 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylococcus capsulatus (bacteria) / Strain: ATCC 33009 / NCIMB 11132 / Bath / Gene: mmoB, MCA1196 / Plasmid: pkk223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P18797

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Non-polymers , 2 types, 53 molecules

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


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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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: 2.46 Å3/Da / Density % sol: 50.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES and 15% PEG 20,000 (w/v) ure 298K, pH 6.5, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 21, 2011
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 457504 / Num. obs: 118133 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 50.8 Å2 / Rsym value: 0.185 / Net I/σ(I): 5.8
Reflection shellResolution: 2.9→2.98 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.537 / % possible all: 93.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MMO, 1CKV
Resolution: 2.902→50 Å / SU ML: 0.38 / σ(F): 1.34 / Phase error: 25.59 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2584 5918 5.01 %
Rwork0.2055 --
obs0.2082 118084 95.03 %
all-118133 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 14.342 Å2 / ksol: 0.298 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--12.1402 Å20 Å2-0 Å2
2--9.0761 Å2-0 Å2
3----19.2864 Å2
Refinement stepCycle: LAST / Resolution: 2.902→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39092 0 8 45 39145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00940174
X-RAY DIFFRACTIONf_angle_d0.86254535
X-RAY DIFFRACTIONf_dihedral_angle_d15.62214504
X-RAY DIFFRACTIONf_chiral_restr0.065612
X-RAY DIFFRACTIONf_plane_restr0.0047080
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9024-2.93540.36061880.3053418X-RAY DIFFRACTION88
2.9354-2.96990.3311970.29073781X-RAY DIFFRACTION97
2.9699-3.00610.3472070.28133754X-RAY DIFFRACTION97
3.0061-3.04420.35032200.27853772X-RAY DIFFRACTION97
3.0442-3.08430.33371790.27063780X-RAY DIFFRACTION97
3.0843-3.12650.34951910.26753802X-RAY DIFFRACTION97
3.1265-3.17120.31921790.26223759X-RAY DIFFRACTION97
3.1712-3.21850.36071960.25093823X-RAY DIFFRACTION97
3.2185-3.26880.28422230.24283718X-RAY DIFFRACTION97
3.2688-3.32240.34392090.23853758X-RAY DIFFRACTION97
3.3224-3.37970.29752160.23063755X-RAY DIFFRACTION97
3.3797-3.44120.28482020.22273759X-RAY DIFFRACTION96
3.4412-3.50740.28981960.21323777X-RAY DIFFRACTION96
3.5074-3.5790.23391910.20083741X-RAY DIFFRACTION96
3.579-3.65680.262170.19953726X-RAY DIFFRACTION95
3.6568-3.74190.25692050.19853758X-RAY DIFFRACTION96
3.7419-3.83540.23672000.19283754X-RAY DIFFRACTION96
3.8354-3.93910.21211960.1793730X-RAY DIFFRACTION96
3.9391-4.05510.252030.18063736X-RAY DIFFRACTION95
4.0551-4.1860.2191890.16593748X-RAY DIFFRACTION95
4.186-4.33560.22031880.16823729X-RAY DIFFRACTION95
4.3356-4.50920.21111840.16953757X-RAY DIFFRACTION95
4.5092-4.71440.2152130.16853720X-RAY DIFFRACTION95
4.7144-4.9630.231910.17153735X-RAY DIFFRACTION95
4.963-5.27390.22811980.18343744X-RAY DIFFRACTION94
5.2739-5.68120.24371860.19463706X-RAY DIFFRACTION93
5.6812-6.25290.2442080.20313718X-RAY DIFFRACTION93
6.2529-7.15770.22571890.20023716X-RAY DIFFRACTION93
7.1577-9.01780.18391690.1643736X-RAY DIFFRACTION92
9.0178-147.95270.21461880.19923756X-RAY DIFFRACTION89
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.27860.20910.53671.36130.73231.6524-0.210.10420.0996-0.14260.0830.0146-0.1689-0.09660.07490.08550.02640.03670.22250.04970.2102-3.5618-53.6981-24.797
20.64770.06930.220.2518-0.42091.0770.04860.04990.0740.0385-0.0393-0.10610.09130.0873-0.00730.13540.0158-0.00580.1136-0.01580.161825.2051-59.8879-8.4229
31.1765-0.19020.01310.59170.35120.9985-0.02170.0930.09740.0767-0.084-0.02340.00620.09260.09210.1451-0.0176-0.00490.11310.00890.187329.0401-51.3509-3.8518
42.4878-0.2305-1.11860.30330.38121.16550.0476-0.17650.32710.090.05190.0009-0.00090.1927-0.08630.1891-0.031-0.01720.20450.00310.200536.1449-44.81123.848
51.954-0.1603-0.88960.43750.13471.1955-0.1290.1742-0.3971-0.0359-0.0989-0.09620.17140.06640.19550.21870.0054-0.0380.3652-0.05160.340525.2457-72.9805-6.0085
60.5168-0.3087-0.244-0.28880.62890.41090.1222-0.0169-0.005-0.11730.0113-0.06840.2274-0.1001-0.08130.15530.0077-0.01440.19420.03740.2275.8334-61.6727-19.6834
70.23720.4769-0.35840.4713-0.02470.7716-0.06140.0964-0.0940.070.02880.00720.1613-0.05240.01770.2063-0.00360.02890.2357-0.00510.2181-4.9489-72.1814-11.8708
80.24540.2002-0.41620.5575-0.14760.56840.02510.0492-0.0148-0.0206-0.01020.1219-0.0484-0.2009-0.01470.15840.0316-0.02280.5201-0.0060.2101-22.7456-59.6004-8.8987
90.46410.1296-0.84790.0726-0.04512.4243-0.02210.08890.03630.09-0.14550.3613-0.0948-0.37720.12180.2170.42960.20520.44730.1270.5096-14.0227-40.84971.3661
100.0804-0.2704-0.06881.16020.80492.31930.0710.29450.51210.18160.02340.0646-0.383-0.2752-0.04440.20120.20310.10640.54770.08350.4092-6.5391-36.377213.4857
112.36781.60180.02971.3551-0.25240.2093-0.1603-0.24340.1396-0.22210.08250.0397-0.0953-0.24370.04580.17340.0427-0.01260.30440.03790.2755-6.797-49.270317.6119
122.97511.28731.59060.48880.68350.8553-0.0195-0.14830.09910.4027-0.09360.0375-0.1830.26320.0320.1383-0.0370.01890.3473-0.08320.23321.0222-43.235211.6463
130.95541.00570.01795.8442-0.33211.2580.00350.2546-0.08130.39160.1449-0.13870.03060.0068-0.0630.12750.0243-0.00760.2477-0.00980.152312.1771-54.647322.1649
143.27843.05840.19644.22690.77710.46420.065-0.5693-0.02620.2121-0.0621-0.1259-0.06250.18810.00460.17920.0038-0.04160.2459-0.07890.15951.4577-59.963218.8693
152.13990.6068-0.46480.3232-0.45650.6735-0.0262-0.2354-0.1314-0.2330.0246-0.1562-0.1168-0.2146-0.0270.24280.04540.00390.1441-0.06930.15917.7718-65.442614.4775
160.00260.0084-0.0003-0.0039-0.0042-0.00440.17580.2503-0.31610.10560.1967-0.11970.38350.1024-0.22240.5431-0.09830.17530.3951-0.09650.6132-6.8194-80.690711.8871
175.66662.23923.11712.85783.68734.78950.2092-0.0401-0.42390.4827-0.3418-0.16210.47130.06510.03610.3992-0.0294-0.00110.25170.12560.4179-16.0481-75.61116.4003
182.9241-0.61610.27064.5782.45345.06680.02920.0076-0.1011-0.202-0.18450.36070.0685-0.47030.21820.4997-0.12270.18410.2217-0.24910.3261-24.7638-70.430510.9785
194.0373-0.63091.20821.7304-0.59691.53950.13060.0973-0.30880.1356-0.1449-0.02110.3354-0.4314-0.00650.4468-0.027-0.0070.2895-0.0150.3362-11.9975-89.3447-18.2849
201.42050.5858-0.24171.4951-0.46090.8502-0.02710.1624-0.29460.05870.1284-0.09370.1026-0.0034-0.09550.34760.03980.06420.2648-0.04190.311611.2023-82.4887-27.0032
213.1263-0.8244-0.25632.62650.58832.284-0.3442-0.3251-0.29710.09660.12420.512-0.1504-0.1760.17090.1774-0.0163-0.00880.38530.05590.1467-4.049-67.2596-48.9198
223.1934-0.681.14641.21621.4413.02090.48780.1534-0.8590.21850.10640.26870.4810.1107-0.3120.36710.07050.08110.2674-0.05410.100826.4795-74.9921-50.046
230.0608-0.04320.09270.14540.1340.2330.05860.0683-0.01870.01810.0295-0.04030.06220.1145-0.06740.22220.0610.02840.3007-0.01460.191933.8495-59.8887-45.2202
240.44780.0740.45290.57030.9461.33410.12660.27230.09190.1218-0.0991-0.1183-0.05970.0218-0.01390.156-0.00070.02760.36980.02760.211643.0996-46.4228-37.5255
250.5066-0.08140.17550.54370.2291.2049-0.04190.1663-0.04460.1120.02130.11890.21850.3035-0.00370.0970.0581-0.04770.4438-0.00540.256647.3247-58.3832-39.5804
260.8284-0.298-0.38470.78141.00970.95811.37720.2162-0.29430.09430.04710.3788-0.22521.1595-0.2546-1.3940.66160.380.56310.03590.082857.2743-59.4858-45.2061
270.5566-0.51060.0932.58411.37872.07420.12620.6228-0.15110.1152-0.1984-0.33180.35280.0849-0.03670.18260.0409-0.23330.7545-0.011-0.212259.4396-59.6263-28.6481
283.67481.44121.12962.78741.16422.31080.18940.3915-0.1318-0.2212-0.0679-0.51550.08930.4355-0.09080.22390.1230.06270.53340.04090.342362.5711-63.5005-38.9597
291.0754-0.2979-0.51980.92610.37242.52590.06640.11610.10370.04810.0315-0.0659-0.3914-0.044-0.13160.21410.0296-0.03540.41740.06340.24135.9615-40.2184-44.6746
30-0.0635-0.16620.10880.29590.12520.5378-0.0113-0.04590.0011-0.05860.0101-0.03170.07010.1652-0.00670.1450.03170.00730.1713-0.01380.19518.303-57.5164-52.7499
310.61660.2584-0.03171.2444-0.15030.7946-0.00130.1995-0.0437-0.0030.02560.0351-0.0181-0.0963-0.03720.14920.0138-0.0180.2739-0.00820.1967.4672-58.1425-72.2099
320.41080.2077-0.51080.86-0.0551.246-0.05490.2084-0.2038-0.1363-0.0029-0.16950.2553-0.03030.05580.19350.0462-0.04470.2795-0.04360.234117.4598-72.7999-75.0064
330.9638-0.3961-0.82171.1734-0.0511.62540.01830.2416-0.3223-0.13110.0461-0.1870.1253-0.0581-0.02210.36050.09280.10590.7377-0.04390.357344.3088-76.7733-75.6572
341.0291-0.25590.15320.3587-0.28810.6403-0.09960.1433-0.0009-0.03630.0027-0.0266-0.01180.23030.11160.24640.08640.00540.6782-0.05610.200247.6046-61.8643-73.2911
352.090.07742.31211.07910.30962.5419-0.27060.02160.301-0.0847-0.0533-0.0196-0.2690.31930.31420.18170.00530.03340.45980.04760.196433.1833-49.4778-79.937
360.51310.29330.630.42690.45321.7389-0.1254-0.02990.0714-0.04620.07050.0589-0.2909-0.50530.02130.19430.04680.04580.28560.03830.23291.637-41.4109-57.8005
371.3965-0.83621.04093.3227-1.57441.1021-0.1374-0.15910.81530.52130.05990.5126-0.4637-0.22420.09040.36560.11950.02710.3443-0.10710.38171.6684-32.3395-41.5645
381.2578-0.0884-0.40721.1689-0.57611.62530.0179-0.50090.0305-0.029-0.139-0.059-0.01960.14240.11520.15030.0093-0.02950.29090.01860.258111.0109-40.8598-42.003
390.70741.06540.85781.58441.28991.04440.0532-0.26680.42310.2643-0.1229-0.7168-0.59740.5780.04780.60160.04670.0660.15360.0540.502919.7651-29.3915-55.2578
400.89090.2052-0.31680.37230.11071.3180.0513-0.2476-0.00090.02750.00420.0396-0.0526-0.1459-0.05310.29210.0547-0.00390.3295-0.0480.3001-15.2916-16.839-27.972
410.56210.32770.02341.15940.37750.95930.0871-0.1473-0.08110.0658-0.1089-0.2143-0.1031-0.32720.04850.27990.06320.02190.27250.04960.21620.736-3.3966-38.4625
420.34320.04-0.26670.689-0.05840.22610.11850.28020.15720.1553-0.0968-0.1872-0.1829-0.1262-0.00870.61210.01090.0250.28940.09990.34511.795412.1305-43.0852
431.34550.78730.28870.6212-0.14150.15630.25210.01050.03780.4968-0.0372-0.0285-0.0612-0.186-0.08110.36590.0433-0.02060.2610.06180.23885.74527.2692-38.1341
440.88270.88660.98890.77440.9641.08590.24820.13830.04650.5536-0.3106-0.4217-0.47690.51630.08570.5176-0.0021-0.03610.48270.22370.417212.711221.3289-47.3861
450.9767-0.75260.56281.28060.21280.98190.03790.44660.1095-0.7249-0.4143-0.2241-0.0421-0.39950.11890.59580.03670.1776-0.09960.27310.316.31390.9161-54.9837
460.462-0.27730.18380.1494-0.08470.0648-0.07570.21280.27550.1886-0.06890.0915-0.36380.06710.07420.4750.0330.08350.41830.09360.353122.40057.796-42.2438
470.51320.70031.08141.98970.4070.67070.11830.0085-0.11670.0489-0.0477-0.1687-0.03390.1056-0.0670.36020.07980.0520.17820.05750.362712.9984-5.5032-48.8161
481.731.67570.65665.97951.86680.70590.1922-0.11080.1025-0.09570.0103-0.6367-0.15970.4897-0.11870.3582-0.08680.17040.50140.05570.436129.04163.7853-47.7676
492.30250.4759-0.2232.28580.38951.81130.11310.0977-0.3776-0.1965-0.2425-0.4337-0.34630.38570.09730.37920.014-0.00430.32160.00020.21225.0728-4.2497-55.8661
500.33790.00190.18710.66530.32881.1994-0.0797-0.24120.32490.139-0.2792-0.0767-0.3671-0.55770.29550.70370.12410.02390.4373-0.00650.4858-2.416315.5399-43.6903
510.55920.8689-0.83590.9919-1.03011.07920.0987-0.166-0.19760.0919-0.1143-0.2755-0.2692-0.05260.00160.49120.0935-0.04720.29360.00930.3-9.7213-3.8174-19.7194
520.47520.6038-0.64470.4115-0.3150.8359-0.0003-0.06770.1987-0.02220.09150.07180.12880.0963-0.02630.45130.0545-0.01420.28730.00090.3294-13.1022-4.8974-35.437
530.7019-0.0148-0.08380.13030.36290.7418-0.0892-0.02160.0548-0.1158-0.02040.1117-0.3751-0.44720.09660.38770.1382-0.02020.56150.01510.3404-22.4752-2.8007-38.4627
540.6467-0.13720.29040.87220.44250.424-0.0273-0.14020.1992-0.068-0.03260.3083-0.2608-0.34330.05490.43360.2067-0.0240.6086-0.06680.4068-36.4133-6.0412-33.3169
550.37890.1952-0.13660.9346-0.49011.2321-0.12280.1650.1299-0.01110.11910.29220.012-0.6478-0.02350.31020.0141-0.05470.6892-0.06950.4251-39.167-19.3611-44.5155
561.193-0.20850.34750.90510.42031.17650.25310.1545-0.16960.0553-0.06950.14120.4292-0.1964-0.21990.3796-0.0492-0.00420.436-0.04430.3844-26.9928-29.0157-41.2083
571.2624-0.5467-0.21120.95250.91443.40290.0216-0.6124-0.3096-0.6443-0.0173-0.29410.4255-0.2015-0.06270.32070.1224-0.0050.38620.00550.4252-10.2844-32.3588-59.7925
585.1112-1.90350.96322.27880.58350.73880.13450.6674-0.0818-0.4547-0.4872-0.01290.1028-0.47510.16870.29990.06550.00890.5368-0.01710.2608-9.8025-22.2514-70.3211
591.1513-0.026-0.41080.91170.66340.62180.3447-0.2477-0.5126-0.1936-0.318-0.34790.07760.3789-0.06430.3180.0645-0.0410.4325-0.04580.3906-21.9227-21.8661-63.6492
601.43110.4371-0.17751.456-0.04160.93240.06580.19680.1049-0.4889-0.18210.174-0.07450.09730.0940.4140.1173-0.00580.3993-0.05420.213-0.2318-17.5359-65.9354
610.1560.0134-0.36450.33420.10420.85690.01140.32780.46430.0654-0.25640.4093-0.1932-0.24670.21380.630.1864-0.04010.3316-0.00990.5377-12.04490.0327-73.6269
623.0330.3588-2.24241.96841.25142.85980.13440.48310.2249-0.4866-0.06440.1986-0.05330.0461-0.0370.51910.1244-0.05960.65520.01940.2914-18.2048-7.1547-69.3972
632.62020.5777-0.12130.0791-0.11770.7242-0.2725-0.11110.2604-0.15710.14220.0749-0.2852-0.22380.11470.41710.1037-0.05130.258-0.04610.2554-10.8291-3.2758-64.5291
642.08962.2930.75675.3238-0.21051.5126-0.0218-0.2780.470.13750.0932-0.0555-0.48260.1228-0.00270.99540.2084-0.15040.50020.01740.6617-33.28853.7726-61.4643
652.52890.05160.04051.67321.90562.4364-0.00250.07470.2749-0.142-0.00280.0710.0887-0.1058-0.04460.42920.1315-0.27841.09180.0380.5164-38.7464-10.0512-65.157
661.02781.1888-0.37751.3674-0.32410.1219-0.07150.25160.54130.19260.08250.0796-0.2961-0.21630.05140.53280.1861-0.15861.08350.01890.7985-42.52377.992-31.4795
670.4969-0.03330.41420.2195-0.27350.48690.0667-0.07860.17870.1098-0.0040.1827-0.32810.012-0.04140.70550.10850.07540.63-0.03020.515-19.374815.303-21.8039
681.84131.0810.05461.83130.06880.5519-0.28230.1935-0.2756-0.40160.16860.6422-0.3314-0.62640.09110.61140.18960.0020.46870.06840.2274-23.5508-6.35-0.6406
691.6070.3192-0.46211.61480.07250.1063-0.1848-0.01420.23240.19130.37120.0272-0.4103-0.4132-0.07950.71960.10230.05030.34810.02750.3141-0.986717.19755.0957
700.4346-0.20250.08380.4203-0.28661.1411-0.0148-0.03110.09490.1748-0.1541-0.0951-0.43750.02150.08910.412-0.0529-0.03810.20910.05530.303511.78719.5782-5.3595
710.9951-0.00830.32250.6768-0.44740.3708-0.11630.21120.08590.0638-0.0199-0.1988-0.08180.46160.15990.3726-0.0474-0.00780.38880.01560.246625.00064.6732-13.5155
720.2435-0.12830.14440.4387-0.55521.2447-0.04610.05910.0836-0.091-0.09930.0477-0.35110.79540.15790.4213-0.1335-0.05170.50910.09540.384731.377310.0664-11.7036
730.76080.1441-0.16080.84340.5520.71220.11340.11740.32570.3684-0.0173-0.2325-0.36820.0431-0.07490.6751-0.0459-0.06580.3480.08640.384522.968121.4181-6.2879
742.0374-1.2373-1.3412.00671.06062.0095-0.00290.1575-0.0690.2869-0.2124-0.4215-0.5197-0.06780.13730.673-0.2596-0.11520.69440.12360.380934.486622.7414-21.157
754.0001-0.2368-2.0411.66730.30152.00220.2407-0.09530.3844-0.3266-0.1524-0.5843-0.57730.4625-0.07770.6531-0.2389-0.06620.53090.11540.698533.965429.1069-10.7416
760.35640.1779-0.29320.7024-0.99571.23790.0042-0.0703-0.1006-0.04370.0201-0.00580.37310.51060.04370.3308-0.049-0.04850.3950.02370.422125.121-5.4541-5.035
770.1731-0.0001-0.40050.26460.12110.57-0.05140.1286-0.0508-0.04030.0935-0.0699-0.4864-0.1317-0.08420.52940.1671-0.01170.2303-0.02670.3683-2.92850.329-1.8131
782.6718-0.2403-0.9431-0.0550.32110.6046-0.1235-0.35540.2218-0.01470.03890.0589-0.52910.13810.09960.58960.0917-0.02570.16880.00570.32124.79741.7576-1.2978
790.02160.1149-0.10270.2416-0.12910.03840.25970.0449-0.0613-0.2576-0.17620.0009-0.1881-0.0312-0.07660.59660.08030.01240.3635-0.00010.26840.18694.981612.7211
800.13490.15690.13780.96060.50670.5384-0.0405-0.037-0.11960.1708-0.0135-0.0675-0.2224-0.03070.03710.40290.0693-0.00490.17560.03660.26670.5104-10.98613.2907
810.7919-0.2786-0.23861.1044-0.16490.8680.0728-0.13340.17570.20390.16370.2013-0.3051-0.5727-0.21950.46590.18630.02960.6385-0.04080.3145-22.3184-2.078323.6993
820.36510.03420.0930.7942-0.0430.1788-0.2047-0.20160.06540.24010.02420.0802-0.18870.05730.11470.68450.11690.01510.4564-0.02660.2499-0.14020.529533.1927
831.9231-0.67961.02230.4709-0.33510.8466-0.4314-0.16120.06690.18510.15510.0276-0.5313-0.34580.2650.66270.20670.0440.4794-0.05790.3326-7.618514.951821.8449
842.19720.35761.8770.70520.71122.6397-0.5312-0.1070.46810.235-0.03820.1708-0.36760.02970.30120.96560.41920.0950.811-0.08090.2802-19.881412.524724.5989
850.5314-0.04270.80871.95091.21722.0247-0.0531-0.0760.48420.20410.00550.1640.1126-0.0357-0.0570.89350.1004-0.05050.4769-0.04060.28066.147731.837224.1782
860.5589-0.96850.34171.7731-0.7461.7779-0.431-0.07910.19760.19810.4271-0.250.3111-0.13610.04720.9666-0.0376-0.1880.5367-0.08220.420713.768822.526430.4016
870.6762-0.1111-0.23860.3798-0.00020.2193-0.157-0.17090.05570.23350.0975-0.1248-0.34140.0370.06560.8213-0.134-0.11560.7610.02960.352324.976819.2722.1612
880.33220.2599-0.45750.39710.08040.817-0.0837-0.1643-0.1270.1570.1958-0.0936-0.0580.2739-0.10050.63940.0226-0.10940.69840.03140.270718.19023.076829.067
890.71840.55740.89940.94490.45991.208-0.0784-0.2652-0.12760.1-0.14640.12010.2629-0.23440.10140.270.03380.04440.44660.02080.4202-8.402-26.234915.5557
901.2892-0.33110.86731.4091-0.09774.2306-0.1809-0.2958-0.0245-0.11130.097-0.01450.2796-0.5247-0.05170.32230.11470.06260.1842-0.00250.2851-0.3588-21.75212.2787
910.7234-1.97441.57245.2423-4.16433.30670.15590.2242-0.4685-0.7507-0.1113-0.02120.683-0.22070.01790.34920.0105-0.05680.2607-0.05460.38691.3599-31.0806-8.0736
921.00750.53510.17440.4711-0.47592.2628-0.22570.24170.10260.06310.2676-0.1279-0.41550.09410.01930.44150.1385-0.04420.08590.00080.33461.7105-19.129-9.2595
931.94580.0675-0.26912.8121-0.18114.92670.3871-0.0661-0.21460.26560.0881-0.2863-0.3740.2647-0.35410.3249-0.021-0.0160.17730.04660.381412.2226-19.6537-1.1177
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resseq 2:63)
2X-RAY DIFFRACTION2chain 'B' and (resseq 64:224)
3X-RAY DIFFRACTION3chain 'B' and (resseq 225:309)
4X-RAY DIFFRACTION4chain 'B' and (resseq 310:389)
5X-RAY DIFFRACTION5chain 'A' and (resseq 15:63)
6X-RAY DIFFRACTION6chain 'A' and (resseq 64:161)
7X-RAY DIFFRACTION7chain 'A' and (resseq 162:352)
8X-RAY DIFFRACTION8chain 'A' and (resseq 353:526)
9X-RAY DIFFRACTION9chain 'C' and (resseq 3:9)
10X-RAY DIFFRACTION10chain 'C' and (resseq 10:24)
11X-RAY DIFFRACTION11chain 'C' and (resseq 25:52)
12X-RAY DIFFRACTION12chain 'C' and (resseq 53:69)
13X-RAY DIFFRACTION13chain 'C' and (resseq 70:103)
14X-RAY DIFFRACTION14chain 'C' and (resseq 104:124)
15X-RAY DIFFRACTION15chain 'C' and (resseq 125:143)
16X-RAY DIFFRACTION16chain 'C' and (resseq 144:151)
17X-RAY DIFFRACTION17chain 'C' and (resseq 152:159)
18X-RAY DIFFRACTION18chain 'C' and (resseq 160:168)
19X-RAY DIFFRACTION19chain 'D' and (resseq 2:36)
20X-RAY DIFFRACTION20chain 'D' and (resseq 37:133)
21X-RAY DIFFRACTION21chain 'G' and (resseq 2:33)
22X-RAY DIFFRACTION22chain 'G' and (resseq 34:61)
23X-RAY DIFFRACTION23chain 'G' and (resseq 62:137)
24X-RAY DIFFRACTION24chain 'G' and (resseq 138:224)
25X-RAY DIFFRACTION25chain 'G' and (resseq 225:309)
26X-RAY DIFFRACTION26chain 'G' and (resseq 310:341)
27X-RAY DIFFRACTION27chain 'G' and (resseq 342:366)
28X-RAY DIFFRACTION28chain 'G' and (resseq 367:389)
29X-RAY DIFFRACTION29chain 'F' and (resseq 15:63)
30X-RAY DIFFRACTION30chain 'F' and (resseq 64:260)
31X-RAY DIFFRACTION31chain 'F' and (resseq 261:441)
32X-RAY DIFFRACTION32chain 'F' and (resseq 442:526)
33X-RAY DIFFRACTION33chain 'H' and (resseq 4:39)
34X-RAY DIFFRACTION34chain 'H' and (resseq 40:124)
35X-RAY DIFFRACTION35chain 'H' and (resseq 125:169)
36X-RAY DIFFRACTION36chain 'I' and (resseq 2:54)
37X-RAY DIFFRACTION37chain 'I' and (resseq 55:68)
38X-RAY DIFFRACTION38chain 'I' and (resseq 69:126)
39X-RAY DIFFRACTION39chain 'I' and (resseq 127:133)
40X-RAY DIFFRACTION40chain 'L' and (resseq 2:73)
41X-RAY DIFFRACTION41chain 'L' and (resseq 74:130)
42X-RAY DIFFRACTION42chain 'L' and (resseq 131:172)
43X-RAY DIFFRACTION43chain 'L' and (resseq 173:203)
44X-RAY DIFFRACTION44chain 'L' and (resseq 204:224)
45X-RAY DIFFRACTION45chain 'L' and (resseq 225:251)
46X-RAY DIFFRACTION46chain 'L' and (resseq 252:275)
47X-RAY DIFFRACTION47chain 'L' and (resseq 276:338)
48X-RAY DIFFRACTION48chain 'L' and (resseq 339:366)
49X-RAY DIFFRACTION49chain 'L' and (resseq 367:389)
50X-RAY DIFFRACTION50chain 'K' and (resseq 15:63)
51X-RAY DIFFRACTION51chain 'K' and (resseq 64:96)
52X-RAY DIFFRACTION52chain 'K' and (resseq 97:160)
53X-RAY DIFFRACTION53chain 'K' and (resseq 161:291)
54X-RAY DIFFRACTION54chain 'K' and (resseq 292:378)
55X-RAY DIFFRACTION55chain 'K' and (resseq 379:459)
56X-RAY DIFFRACTION56chain 'K' and (resseq 460:526)
57X-RAY DIFFRACTION57chain 'M' and (resseq 4:24)
58X-RAY DIFFRACTION58chain 'M' and (resseq 25:39)
59X-RAY DIFFRACTION59chain 'M' and (resseq 40:52)
60X-RAY DIFFRACTION60chain 'M' and (resseq 53:86)
61X-RAY DIFFRACTION61chain 'M' and (resseq 87:103)
62X-RAY DIFFRACTION62chain 'M' and (resseq 104:118)
63X-RAY DIFFRACTION63chain 'M' and (resseq 119:143)
64X-RAY DIFFRACTION64chain 'M' and (resseq 144:151)
65X-RAY DIFFRACTION65chain 'M' and (resseq 152:165)
66X-RAY DIFFRACTION66chain 'N' and (resseq 2:36)
67X-RAY DIFFRACTION67chain 'N' and (resseq 37:129)
68X-RAY DIFFRACTION68chain 'Q' and (resseq 2:32)
69X-RAY DIFFRACTION69chain 'Q' and (resseq 33:73)
70X-RAY DIFFRACTION70chain 'Q' and (resseq 74:130)
71X-RAY DIFFRACTION71chain 'Q' and (resseq 131:203)
72X-RAY DIFFRACTION72chain 'Q' and (resseq 204:276)
73X-RAY DIFFRACTION73chain 'Q' and (resseq 277:338)
74X-RAY DIFFRACTION74chain 'Q' and (resseq 339:366)
75X-RAY DIFFRACTION75chain 'Q' and (resseq 367:389)
76X-RAY DIFFRACTION76chain 'P' and (resseq 15:63)
77X-RAY DIFFRACTION77chain 'P' and (resseq 64:127)
78X-RAY DIFFRACTION78chain 'P' and (resseq 128:161)
79X-RAY DIFFRACTION79chain 'P' and (resseq 162:204)
80X-RAY DIFFRACTION80chain 'P' and (resseq 205:352)
81X-RAY DIFFRACTION81chain 'P' and (resseq 353:410)
82X-RAY DIFFRACTION82chain 'P' and (resseq 411:459)
83X-RAY DIFFRACTION83chain 'P' and (resseq 460:497)
84X-RAY DIFFRACTION84chain 'P' and (resseq 498:526)
85X-RAY DIFFRACTION85chain 'R' and (resseq 4:25)
86X-RAY DIFFRACTION86chain 'R' and (resseq 26:52)
87X-RAY DIFFRACTION87chain 'R' and (resseq 53:118)
88X-RAY DIFFRACTION88chain 'R' and (resseq 119:169)
89X-RAY DIFFRACTION89chain 'S' and (resseq 2:25)
90X-RAY DIFFRACTION90chain 'S' and (resseq 26:54)
91X-RAY DIFFRACTION91chain 'S' and (resseq 55:68)
92X-RAY DIFFRACTION92chain 'S' and (resseq 69:108)
93X-RAY DIFFRACTION93chain 'S' and (resseq 109:133)

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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