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- PDB-3h4y: Crystal structure of putative chemotaxis protein (YP_009526.1) fr... -

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Basic information

Entry
Database: PDB / ID: 3h4y
TitleCrystal structure of putative chemotaxis protein (YP_009526.1) from DESULFOVIBRIO VULGARIS HILDENBOROUGH at 1.55 A resolution
Componentsputative chemotaxis protein
KeywordsHYDROLASE / YP_009526.1 / putative chemotaxis protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


CheY-P phosphatase CheX-like / Chemotaxis phosphatase CheX-like domain / Chemotaxis phosphatase CheX / CheC-like / Chemotaxis protein chec / CheC-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Chemotaxis protein CheX, putative
Similarity search - Component
Biological speciesDesulfovibrio vulgaris str. Hildenborough (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative chemotaxis protein (YP_009526.1) from DESULFOVIBRIO VULGARIS HILDENBOROUGH at 1.55 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: putative chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9533
Polymers16,6431
Non-polymers3102
Water2,504139
1
A: putative chemotaxis protein
hetero molecules

A: putative chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9066
Polymers33,2862
Non-polymers6214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3630 Å2
ΔGint-1 kcal/mol
Surface area12150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.820, 43.820, 158.604
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein putative chemotaxis protein / Chemotaxis protein CheX / putative


Mass: 16642.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris str. Hildenborough (bacteria)
Gene: DVU_0302, YP_009526.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q72FB2
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.29 Å3/Da / Density % sol: 46.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 10.0000% MPD, 0.1M Citrate pH 4.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97904
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 26, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97904 Å / Relative weight: 1
ReflectionResolution: 1.55→29.399 Å / Num. obs: 23188 / % possible obs: 99.1 % / Redundancy: 12.3 % / Biso Wilson estimate: 17.632 Å2 / Rmerge(I) obs: 0.113 / Rsym value: 0.113 / Net I/σ(I): 4.79
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.55-1.597.30.9350.81176516210.93597.5
1.59-1.637.20.80111174716310.80198.2
1.63-1.687.20.6691.11135715680.66998.5
1.68-1.737.30.5641.31116015190.56498.5
1.73-1.7910.10.5791.31498714770.57998.7
1.79-1.85110.4831.51601314580.48398.9
1.85-1.9212.10.3681.91716214160.36899.1
1.92-2140.2852.51905613650.28599.1
2-2.0915.80.23932052212990.23999.3
2.09-2.1915.90.1943.72005512650.19499.5
2.19-2.3115.90.1683.91899411980.16899.5
2.31-2.4515.70.1451795911430.1499.7
2.45-2.6215.70.1285.51675110700.12899.7
2.62-2.8315.50.1076.51586710230.10799.9
2.83-3.115.50.0847.9147229480.08499.9
3.1-3.4715.20.0738.7130528570.07399.9
3.47-415.10.0699116517730.06999.9
4-4.914.70.0659.2100086810.065100
4.9-6.9313.80.0738.174365380.073100
6.93-29.4111.80.0591039923380.05998.4

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.55→29.399 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 2.894 / SU ML: 0.046 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.076
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3.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. 4.CIT (CITRATE) AND (4R)-2-METHYLPENTANE-2,4-DIOL (MRD) FROM THE CRYSTALLIZATION AND CRYOPROTECTION CONDITIONS HAVE BEEN MODELED IN THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.196 1191 5.1 %RANDOM
Rwork0.162 ---
obs0.163 23154 98.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.01 Å2 / Biso mean: 16.565 Å2 / Biso min: 3.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20 Å2
2--0.25 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.55→29.399 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1115 0 21 139 1275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221207
X-RAY DIFFRACTIONr_bond_other_d0.0010.02778
X-RAY DIFFRACTIONr_angle_refined_deg1.6311.9791651
X-RAY DIFFRACTIONr_angle_other_deg0.93131952
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.255172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.09926.31638
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.13415211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.648151
X-RAY DIFFRACTIONr_chiral_restr0.0950.2200
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211350
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02207
X-RAY DIFFRACTIONr_mcbond_it1.5893790
X-RAY DIFFRACTIONr_mcbond_other0.4343327
X-RAY DIFFRACTIONr_mcangle_it2.71951292
X-RAY DIFFRACTIONr_scbond_it4.5378417
X-RAY DIFFRACTIONr_scangle_it7.02311349
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 92 -
Rwork0.271 1540 -
all-1632 -
obs--97.14 %
Refinement TLS params.Method: refined / Origin x: 12.1943 Å / Origin y: 5.2364 Å / Origin z: 10.5058 Å
111213212223313233
T0.0096 Å20.0022 Å20.0051 Å2-0.0592 Å2-0.0048 Å2--0.0398 Å2
L0.1283 °20.0227 °2-0.19 °2-0.497 °2-0.0963 °2--0.9723 °2
S-0.0178 Å °-0.074 Å °0.0196 Å °-0.0507 Å °0.0356 Å °-0.0287 Å °0.0567 Å °0.0453 Å °-0.0178 Å °

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