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- PDB-2ich: CRYSTAL STRUCTURE OF A PUTATIVE ATTH (NE1406) FROM NITROSOMONAS E... -

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Entry
Database: PDB / ID: 2ich
TitleCRYSTAL STRUCTURE OF A PUTATIVE ATTH (NE1406) FROM NITROSOMONAS EUROPAEA AT 2.00 A RESOLUTION
ComponentsPutative AttH
KeywordsLIPID BINDING PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homologyAttH-like fold / AttH-like domain / AttH domain / AttH-like domain superfamily / CrtC N-terminal lipocalin domain / Lipocalin-like domain / Beta Barrel / Mainly Beta / Putative AttH
Function and homology information
Biological speciesNitrosomonas europaea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Structure of the first representative of Pfam family PF09410 (DUF2006) reveals a structural signature of the calycin superfamily that suggests a role in lipid metabolism.
Authors: Chiu, H.J. / Bakolitsa, C. / Skerra, A. / Lomize, A. / Carlton, D. / Miller, M.D. / Krishna, S.S. / Abdubek, P. / Astakhova, T. / Axelrod, H.L. / Clayton, T. / Deller, M.C. / Duan, L. / ...Authors: Chiu, H.J. / Bakolitsa, C. / Skerra, A. / Lomize, A. / Carlton, D. / Miller, M.D. / Krishna, S.S. / Abdubek, P. / Astakhova, T. / Axelrod, H.L. / Clayton, T. / Deller, M.C. / Duan, L. / Feuerhelm, J. / Grant, J.C. / Grzechnik, S.K. / Han, G.W. / Jaroszewski, L. / Jin, K.K. / Klock, H.E. / Knuth, M.W. / Kozbial, P. / Kumar, A. / Marciano, D. / McMullan, D. / Morse, A.T. / Nigoghossian, E. / Okach, L. / Paulsen, J. / Reyes, R. / Rife, C.L. / van den Bedem, H. / Weekes, D. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Elsliger, M.A. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionSep 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 30, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 300 BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative AttH
B: Putative AttH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4938
Polymers75,7072
Non-polymers7876
Water7,098394
1
A: Putative AttH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2494
Polymers37,8531
Non-polymers3953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative AttH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2454
Polymers37,8531
Non-polymers3913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.275, 95.573, 121.745
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 1 / Refine code: 5

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUALAALAAA24 - 743 - 53
21LEULEUALAALABB24 - 743 - 53
12SERSERVALVALAA83 - 35162 - 330
22SERSERVALVALBB83 - 35162 - 330

NCS ensembles :
ID
1
2
DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Putative AttH


Mass: 37853.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosomonas europaea (bacteria) / Gene: NP_841447.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q82US3
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 47.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 9
Details: 1.4M ammonium sulfate, 0.1M CHES, pH 9.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97939,0.94926,0.97925
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 11, 2006 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal Monochrometer / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979391
20.949261
30.979251
ReflectionResolution: 2→29.161 Å / Num. obs: 49800 / % possible obs: 98.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Net I/σ(I): 5.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.053.50.5991.31242735420.59995.9
2.05-2.113.60.5221.41241234860.52296.8
2.11-2.173.60.4191.81208533880.41996.5
2.17-2.243.50.5111.51147432650.51197.1
2.24-2.313.30.32621060031780.32696.8
2.31-2.393.60.2882.61119031300.28897.4
2.39-2.483.60.2453.11075830060.24598.1
2.48-2.583.60.2053.61060629600.20599
2.58-2.73.60.184.21029128560.1899.3
2.7-2.833.60.1465999627410.146100
2.83-2.983.70.1126.5964126150.112100
2.98-3.163.70.0888925424930.088100
3.16-3.383.70.0769863323280.076100
3.38-3.653.60.088785121600.0899.4
3.65-43.60.087.9719120240.0899.8
4-4.473.70.05810.3670918330.058100
4.47-5.163.60.05510.9596516410.055100
5.16-6.323.60.069.9505914090.06100
6.32-8.943.50.05510.9385411090.055100
8.94-29.163.20.04911.720526360.04996.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→29.161 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.924 / SU B: 9.906 / SU ML: 0.137 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.164
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. RESIDUES A75-82 AND B75-80 ARE DISORDERED AND NOT INCLUDED IN THE MODEL. 4. SEVERAL MOLECULES OF 2-(CYCLOHEXYLAMINO)ETHANESULFONIC ACID, SULFATE ION FROM CRYSTALLIZATION SOLUTION AND GLYCEROL FROM PROTECTANT SOLUTION ARE INCLUDED IN THE MODEL. 5. THERE IS SOME UNMODELLED DENSITY NEAR A125 AND B63 ON THE PROTEIN SURFACE. 6. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.232 2528 5.1 %RANDOM
Rwork0.182 ---
obs0.184 49646 97.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.666 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20 Å20 Å2
2---0.87 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2→29.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5086 0 49 394 5529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0225348
X-RAY DIFFRACTIONr_bond_other_d0.0010.024668
X-RAY DIFFRACTIONr_angle_refined_deg1.6471.9357303
X-RAY DIFFRACTIONr_angle_other_deg0.846310811
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7045655
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.46123.231260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54915777
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3741541
X-RAY DIFFRACTIONr_chiral_restr0.1040.2762
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026075
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021186
X-RAY DIFFRACTIONr_nbd_refined0.1840.2835
X-RAY DIFFRACTIONr_nbd_other0.2030.24793
X-RAY DIFFRACTIONr_nbtor_refined0.1850.22479
X-RAY DIFFRACTIONr_nbtor_other0.0880.23197
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2352
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1170.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2210.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0850.29
X-RAY DIFFRACTIONr_mcbond_it2.28333320
X-RAY DIFFRACTIONr_mcbond_other0.75431323
X-RAY DIFFRACTIONr_mcangle_it3.22855223
X-RAY DIFFRACTIONr_scbond_it5.56382388
X-RAY DIFFRACTIONr_scangle_it7.089112080
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1295MEDIUM POSITIONAL0.180.5
1491LOOSE POSITIONAL0.315
1295MEDIUM THERMAL1.112
1491LOOSE THERMAL2.2710
21566MEDIUM POSITIONAL0.150.5
22408LOOSE POSITIONAL0.465
21566MEDIUM THERMAL1.072
22408LOOSE THERMAL2.4210
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 188 -
Rwork0.239 3351 -
obs-3539 95.44 %
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)
10.8519-0.22780.25531.14050.09670.46890.0141-0.04320.02120.045-0.00360.0346-0.0022-0.0071-0.0105-0.0806-0.00430.0021-0.0334-0.0077-0.0789.45820.616716.7779
21.0715-0.2441-0.19990.98230.1280.5227-0.0053-0.0143-0.0030.0181-0.02030.04720.0334-0.03220.0256-0.0542-0.0155-0.014-0.07240.0067-0.091225.292635.405549.549
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA24 - 3513 - 330
22BB24 - 3523 - 331

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