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- PDB-3khn: Crystal structure of putative MotB like protein DVU_2228 from Des... -

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Basic information

Entry
Database: PDB / ID: 3khn
TitleCrystal structure of putative MotB like protein DVU_2228 from Desulfovibrio vulgaris.
ComponentsMotB protein, putative
Keywordsstructural genomics / unknown function / OmpA-like domain / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


Motility protein B-like, N-terminal domain / Membrane MotB of proton-channel complex MotA/MotB / OmpA-like domain / : / OmpA-like domain profile. / OmpA-like domain superfamily / OmpA family / OmpA-like domain / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
MotB protein, putative
Similarity search - Component
Biological speciesDesulfovibrio vulgaris str. Hildenborough (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.03 Å
AuthorsRamagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of putative MotB like protein DVU_2228 from Desulfovibrio vulgaris
Authors: Ramagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C.
History
DepositionOct 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_conn
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MotB protein, putative
B: MotB protein, putative


Theoretical massNumber of molelcules
Total (without water)39,7922
Polymers39,7922
Non-polymers00
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-6 kcal/mol
Surface area15530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.218, 83.709, 85.891
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MotB protein, putative


Mass: 19896.152 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris str. Hildenborough (bacteria)
Strain: Hildenborough / ATCC 29579 / NCIMB 8303 / Gene: DVU_2228 / Plasmid: pSGX4(BC) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q729W9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 1.91 Å3/Da / Density % sol: 35.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Bis-Tris pH 6.5, 30% PEG MME 550 0.05M Calcium Chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. all: 20244 / Num. obs: 20244 / % possible obs: 98.9 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.054 / Rsym value: 0.052 / Net I/σ(I): 30.3
Reflection shellResolution: 2.03→2.07 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.086 / Mean I/σ(I) obs: 22.4 / Num. unique all: 793 / Rsym value: 0.09 / % possible all: 79.9

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SHELXEmodel building
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 2.03→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.907 / WRfactor Rfree: 0.292 / WRfactor Rwork: 0.208 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.835 / SU B: 4.374 / SU ML: 0.123 / SU R Cruickshank DPI: 0.22 / SU Rfree: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1033 5.1 %RANDOM
Rwork0.185 ---
obs0.189 20197 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 68.97 Å2 / Biso mean: 21.437 Å2 / Biso min: 6.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å20 Å2
2---0.06 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 2.03→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2548 0 0 171 2719
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222594
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.9593521
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9195324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.68622.878139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.07615430
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6971535
X-RAY DIFFRACTIONr_chiral_restr0.1070.2395
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212035
X-RAY DIFFRACTIONr_mcbond_it0.9841.51601
X-RAY DIFFRACTIONr_mcangle_it1.75122582
X-RAY DIFFRACTIONr_scbond_it2.6453993
X-RAY DIFFRACTIONr_scangle_it4.3844.5937
LS refinement shellResolution: 2.033→2.086 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 73 -
Rwork0.206 1382 -
all-1455 -
obs--99.66 %

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