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- PDB-2pmb: Crystal structure of predicted nucleotide-binding protein from Vi... -

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Basic information

Entry
Database: PDB / ID: 2pmb
TitleCrystal structure of predicted nucleotide-binding protein from Vibrio cholerae
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMICS RESEARCH CONSORTIUM / NYSGRC / New York SGX Research Center for Structural Genomics / NYSGXRC
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 ...: / 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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.99 Å
AuthorsPatskovsky, Y. / Zhan, C. / Shi, W. / Toro, R. / Sauder, J.M. / Gilmore, J. / Iizuka, M. / Maletic, M. / Gheyi, T. / Wasserman, S.R. ...Patskovsky, Y. / Zhan, C. / Shi, W. / Toro, R. / Sauder, J.M. / Gilmore, J. / Iizuka, M. / Maletic, M. / Gheyi, T. / Wasserman, S.R. / Smith, D. / 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: Patskovsky, Y. / Zhan, C. / Shi, W. / Sauder, J.M. / Gilmore, J. / Iizuka, M. / Maletic, M. / Gheyi, T. / Wasserman, S.R. / Smith, D. / Burley, S.K. / Almo, S.C.
History
DepositionApr 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,58918
Polymers210,2654
Non-polymers1,32414
Water9,782543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12950 Å2
ΔGint-98 kcal/mol
Surface area63590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.802, 178.222, 89.513
Angle α, β, γ (deg.)90.00, 103.78, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain: (Details: A B C D)
NCS domain segments:

Dom-ID: 1 / Ens-ID: 1 / Beg label comp-ID: SER / End label comp-ID: VAL / Refine code: 1 / Auth seq-ID: 5 - 456 / Label seq-ID: 2 - 453

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

NCS ensembles : (Details: A B C D)

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Components

#1: Protein
Uncharacterized protein / Predicted Rossmann fold nucleotide-binding protein


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


Mass: 94.971 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 543 / 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: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 294 K / pH: 6.2
Details: 0.1M SODIUM-POTASSIUM PHOSPHATE pH 6.2, 20% PEG 1000, 0.2M SODIUM CHLORIDE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 294K, pH 6.20

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97961
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 30, 2007 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97961 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 123599 / % possible obs: 94.8 % / Observed criterion σ(I): -5 / Redundancy: 1.9 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.131 / Rsym value: 0.122 / Net I/σ(I): 3.4
Reflection shellResolution: 1.99→2.1 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 0.6 / Rsym value: 0.58 / % possible all: 83.7

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Processing

Software
NameVersionClassification
SHELXmodel building
REFMAC5.3.0034refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.99→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.921 / SU B: 6.744 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.266 3331 3 %RANDOM
Rwork0.208 ---
obs0.21 106758 90.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20.24 Å2
2---0.43 Å20 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.99→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13720 0 72 543 14335
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02214294
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1811.9819378
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.58251797
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.61724.305669
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.878152547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.95915100
X-RAY DIFFRACTIONr_chiral_restr0.0990.22124
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210838
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1420.36524
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.59575
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.51247
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0980.3128
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.561
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.0112.59038
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.0143.514231
X-RAY DIFFRACTIONr_scbond_it6.97945807
X-RAY DIFFRACTIONr_scangle_it9.31665110
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 3300 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Atight positional0.340.1
Btight positional0.30
Ctight positional0.40
Dtight positional0.370
Atight thermal4.911.5
Btight thermal3.980
Ctight thermal4.960
Dtight thermal4.290
LS refinement shellResolution: 1.99→2.04 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 143 -
Rwork0.314 4833 -
obs--55.86 %

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