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- PDB-3gh1: Crystal structure of predicted nucleotide-binding protein from Vi... -

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Basic information

Entry
Database: PDB / ID: 3gh1
TitleCrystal structure of predicted nucleotide-binding protein from Vibrio cholerae
ComponentsPredicted nucleotide-binding protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / PSI / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


AMP nucleosidase / AMP nucleosidase activity / cytosol
Similarity search - Function
: / MCP/YpsA-like / MoCo carrier protein-like / Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase, C-terminal domain / Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase, N-terminal / Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase PpnN-like superfamily / Pyrimidine/purine nucleotide monophosphate nucleosidase, C-terminal / Pyrimidine/purine nucleotide 5'-monophosphate nucleosidases / LOG family / Possible lysine decarboxylase ...: / MCP/YpsA-like / MoCo carrier protein-like / Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase, C-terminal domain / Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase, N-terminal / Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase PpnN-like superfamily / Pyrimidine/purine nucleotide monophosphate nucleosidase, C-terminal / Pyrimidine/purine nucleotide 5'-monophosphate nucleosidases / LOG family / Possible lysine decarboxylase / Rossmann fold - #450 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / AMP nucleosidase
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsMalashkevich, V.N. / Toro, R. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of predicted nucleotide-binding protein from Vibrio cholerae.
Authors: Malashkevich, V.N. / Toro, R. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionMar 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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 1.5Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Predicted nucleotide-binding protein
B: Predicted nucleotide-binding protein
C: Predicted nucleotide-binding protein
D: Predicted nucleotide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,6458
Polymers210,2654
Non-polymers3804
Water23,9421329
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9370 Å2
ΔGint-20.6 kcal/mol
Surface area67060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.034, 181.546, 95.772
Angle α, β, γ (deg.)90.000, 103.320, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 1 / Auth seq-ID: -999 - 999 / Label seq-ID: -999 - 999

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
Predicted nucleotide-binding protein


Mass: 52566.223 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Strain: El Tor Inaba N16961 / Serotype O1 / Gene: VC_0899 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q9KTK3
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1329 / 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: 2.38 Å3/Da / Density % sol: 48.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.15M Malic acid, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9791 Å
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Mar 27, 2007
RadiationProtocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.832→27.096 Å / Num. obs: 149929 / % possible obs: 88 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.159 / Net I/σ(I): 2.955

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 49.45 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å48.54 Å
Translation3.5 Å48.54 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.2.5data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2PMB

2pmb


Resolution: 1.9→19.92 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.237 / WRfactor Rwork: 0.174 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.869 / SU B: 7.17 / SU ML: 0.095 / SU R Cruickshank DPI: 0.159 / SU Rfree: 0.156 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.226 6921 5 %RANDOM
Rwork0.169 ---
obs0.172 138191 90.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 99.64 Å2 / Biso mean: 22.133 Å2 / Biso min: 4.73 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13957 0 20 1329 15306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02214289
X-RAY DIFFRACTIONr_angle_refined_deg1.9191.97219342
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.18151770
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.12924.195665
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.923152483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0811596
X-RAY DIFFRACTIONr_chiral_restr0.1390.22121
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02110876
X-RAY DIFFRACTIONr_mcbond_it1.6353.58872
X-RAY DIFFRACTIONr_mcangle_it4.6315014297
X-RAY DIFFRACTIONr_scbond_it9.778505417
X-RAY DIFFRACTIONr_scangle_it2.4074.55042
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 3420 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
ATIGHT POSITIONAL0.465
BTIGHT POSITIONAL0.435
CTIGHT POSITIONAL0.525
DTIGHT POSITIONAL0.435
ATIGHT THERMAL3.4810
BTIGHT THERMAL3.110
CTIGHT THERMAL4.2510
DTIGHT THERMAL3.6710
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 369 -
Rwork0.314 7925 -
all-8294 -
obs--74.11 %
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)
10.3811-0.0479-0.09040.22290.00710.25250.03720.01210.1077-0.0312-0.0201-0.0164-0.0697-0.0176-0.01710.0320.0089-0.00320.00320.00120.04688.508129.381816.1012
20.52410.0529-0.05650.43050.02690.36890.0086-0.0574-0.11150.0291-0.018-0.04390.111-0.01740.00930.0429-0.0143-0.01370.01240.02050.038525.4126-30.564629.861
30.7410.241-0.28070.5383-0.15880.33070.0794-0.24810.08850.1111-0.0455-0.0235-0.04250.0644-0.0340.0373-0.0193-0.00940.0886-0.03330.023332.30811.464448.8424
40.53090.0153-0.19880.37870.05670.6121-0.02650.071-0.0316-0.083-0.0109-0.0010.0333-0.07560.03730.0344-0.0068-0.00460.0147-0.00470.008216.4211-10.2615-8.1255
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 462
2X-RAY DIFFRACTION2B2 - 462
3X-RAY DIFFRACTION3C2 - 453
4X-RAY DIFFRACTION4D2 - 454

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