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- PDB-1qyi: X-RAY STRUCTURE OF Q8NW41 NORTHEAST STRUCTURAL GENOMICS CONSORTIU... -

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Basic information

Entry
Database: PDB / ID: 1qyi
TitleX-RAY STRUCTURE OF Q8NW41 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ZR25.
Componentshypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyHAD-hyrolase-like / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / HAD family hydrolase / Uncharacterized protein
Function and homology information
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsKuzin, A.P. / Edstrom, W. / Ma, L.C. / Shin, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: X-RAY STRUCTURE OF Q8NW41 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ZR25.
Authors: Kuzin, A.P. / Edstrom, W. / Ma, L.C. / Shih, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionSep 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein


Theoretical massNumber of molelcules
Total (without water)44,0071
Polymers44,0071
Non-polymers00
Water3,351186
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.480, 87.480, 115.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein hypothetical protein / ZR25


Mass: 44007.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Species: Staphylococcus aureus / Strain: MW2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NW41, UniProt: A0A0H3JXW6*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.51 Å3/Da / Density % sol: 50.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3350, 0.2M Lithium nitrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97942, 0.97922, 0.97236
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 21, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979421
20.979221
30.972361
ReflectionResolution: 2.5→20 Å / Num. all: 27084 / Num. obs: 23940 / % possible obs: 89.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.146 / % possible all: 71.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→19.97 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2866653.65 / Data cutoff high rms absF: 2866653.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.278 1169 4.9 %RANDOM
Rwork0.216 ---
obs0.216 23940 81 %-
all-27084 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 11.2875 Å2 / ksol: 0.256747 e/Å3
Displacement parametersBiso mean: 30.7 Å2
Baniso -1Baniso -2Baniso -3
1-8.88 Å20 Å20 Å2
2--8.88 Å20 Å2
3----17.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3049 0 0 186 3235
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_improper_angle_d0.72
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.354 182 5.2 %
Rwork0.237 3316 -
obs--71.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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