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- PDB-2fi9: The crystal structure of an outer membrane protein from the Barto... -

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Basic information

Entry
Database: PDB / ID: 2fi9
TitleThe crystal structure of an outer membrane protein from the Bartonella henselae
ComponentsOuter membrane protein
KeywordsMEMBRANE PROTEIN / Structural Genomics / Outer membrane protein / Bartonella henselae / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyHypothetical Protein Mth938; Chain: A, / MTH938-like / NDUFAF3/Mth938 domain-containing protein / MTH938-like superfamily / Protein of unknown function (DUF498/DUF598) / 3-Layer(aba) Sandwich / Alpha Beta / : / Hypothetical outer membrane protein
Function and homology information
Biological speciesBartonella henselae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsZhang, R. / Hatzos, C. / Clancy, S. / Collart, F. / Cymborowski, M. / Minor, W. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The 1.8A crystal structure of an outer membrane protein from the Bartonella henselae
Authors: Zhang, R. / Hatzos, C. / Clancy, S. / Collart, F. / Cymborowski, M. / Minor, W. / Joachimiak, A.
History
DepositionDec 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICAL UNIT OF THIS MOLECULE IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer membrane protein


Theoretical massNumber of molelcules
Total (without water)14,0231
Polymers14,0231
Non-polymers00
Water95553
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.527, 51.931, 62.368
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 Outer membrane protein


Mass: 14023.018 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella henselae (bacteria) / Strain: str. Houston-1 / Gene: GI:49238164 / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 49238164, UniProt: Q8RIU4*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 1.99 Å3/Da / Density % sol: 38.28 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 2M (NH4)2SO4, 0.1M CAPS pH10.5, 0.2M Li2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 19, 2005 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. all: 10365 / Num. obs: 8970 / % possible obs: 86.54 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 21
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 1.3 / Num. unique all: 986 / % possible all: 35.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→39.9 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 8.244 / SU ML: 0.12 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.147
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2342 447 4.7 %RANDOM
Rwork0.19927 ---
obs0.2009 8970 86.54 %-
all-10365 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.406 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å20 Å2
2--1.2 Å20 Å2
3----0.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.036 Å0.033 Å
Luzzati d res low-6 Å
Luzzati sigma a0.5 Å0.032 Å
Refinement stepCycle: LAST / Resolution: 1.8→39.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms905 0 0 53 958
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022921
X-RAY DIFFRACTIONr_angle_refined_deg1.3251.9831250
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7665117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.7052340
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.28615153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.855159
X-RAY DIFFRACTIONr_chiral_restr0.0860.2145
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02698
X-RAY DIFFRACTIONr_nbd_refined0.2110.2433
X-RAY DIFFRACTIONr_nbtor_refined0.3070.2662
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.248
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.212
X-RAY DIFFRACTIONr_mcbond_it0.6891.5601
X-RAY DIFFRACTIONr_mcangle_it1.1462943
X-RAY DIFFRACTIONr_scbond_it2.0233354
X-RAY DIFFRACTIONr_scangle_it3.3194.5307
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 15 -
Rwork0.283 292 -
obs--39.46 %
Refinement TLS params.Method: refined / Origin x: 23.07 Å / Origin y: 32.367 Å / Origin z: 23.635 Å
111213212223313233
T0.1491 Å2-0.0062 Å20.0054 Å2--0.1013 Å2-0.0175 Å2---0.2427 Å2
L1.7943 °2-0.5447 °20.9432 °2-1.7642 °2-0.1071 °2--4.1723 °2
S0.0398 Å °0.0247 Å °0.0166 Å °-0.0698 Å °-0.0049 Å °0.0106 Å °0.2253 Å °0.0171 Å °-0.0348 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA11 - 5011 - 50
2X-RAY DIFFRACTION1AA51 - 9051 - 90
3X-RAY DIFFRACTION1AA91 - 12891 - 128

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