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- PDB-2ozz: Crystal structure of YhfZ from Shigella flexneri -

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Basic information

Entry
Database: PDB / ID: 2ozz
TitleCrystal structure of YhfZ from Shigella flexneri
ComponentsHypothetical protein yhfZ
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta structure / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyUncharacterised protein YhfZ, C-terminal domain / YhfZ C-terminal domain / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein YhfZ C-terminal domain-containing protein / YhfZ_C domain-containing protein
Function and homology information
Biological speciesShigella flexneri 2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.298 Å
AuthorsKim, Y. / Borovilos, M. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure of YhfZ from Shigella flexneri
Authors: Kim, Y. / Borovilos, M. / Clancy, S. / Joachimiak, A.
History
DepositionFeb 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 30, 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 / 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
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). AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN. THE BIOLOGICAL UNIT ASSEMBLY SHOWN IN REMARK 350 IS PREDICTED BY THE ANALYSIS OF PROTEIN INTERFACES BASED ON THIS CRYSTAL STRUCTURE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein yhfZ
B: Hypothetical protein yhfZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4636
Polymers52,0792
Non-polymers3844
Water2,990166
1
A: Hypothetical protein yhfZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3284
Polymers26,0391
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical protein yhfZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1352
Polymers26,0391
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.270, 62.550, 170.192
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hypothetical protein yhfZ


Mass: 26039.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri 2a (bacteria) / Species: Shigella flexneri / Strain: 2457T, 301 / Gene: yhfZ, SF3401, S_4361 / Plasmid: MCSG19 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q83JA6, UniProt: A0A0H2V277*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.41 Å3/Da / Density % sol: 49.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M Ammonium sulfate, 0.1 M Sodium citrate, pH 5.6, 20 % PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97912 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 2, 2006 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 2.298→37.71 Å / Num. all: 23138 / Num. obs: 23138 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.3 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 10.1
Reflection shellResolution: 2.298→2.38 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.601 / Mean I/σ(I) obs: 2.21 / Num. unique all: 2186 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.2.0000refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXCDphasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
SOLVEphasing
RESOLVEphasing
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.298→37.71 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.913 / SU B: 16.521 / SU ML: 0.209 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.441 / ESU R Free: 0.295
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: Program CNS 1.2 has also been used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.288 2334 10.2 %RANDOM
Rwork0.222 ---
all0.229 20590 --
obs0.229 20590 98.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.017 Å2
Baniso -1Baniso -2Baniso -3
1--1.34 Å20 Å20 Å2
2--0.01 Å20 Å2
3---1.33 Å2
Refinement stepCycle: LAST / Resolution: 2.298→37.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3586 0 20 166 3772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223676
X-RAY DIFFRACTIONr_angle_refined_deg1.571.9675009
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6215464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.47624.457184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.24415616
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7731527
X-RAY DIFFRACTIONr_chiral_restr0.1020.2559
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022849
X-RAY DIFFRACTIONr_nbd_refined0.2230.21779
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.2235
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2250.212
X-RAY DIFFRACTIONr_mcbond_it0.9911.52352
X-RAY DIFFRACTIONr_mcangle_it1.45223682
X-RAY DIFFRACTIONr_scbond_it2.17931500
X-RAY DIFFRACTIONr_scangle_it3.1834.51327
LS refinement shellResolution: 2.298→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.332 128
Rwork0.247 1350
obs-1499

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