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- PDB-1fx3: CRYSTAL STRUCTURE OF H. INFLUENZAE SECB -

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Basic information

Entry
Database: PDB / ID: 1fx3
TitleCRYSTAL STRUCTURE OF H. INFLUENZAE SECB
ComponentsPROTEIN-EXPORT PROTEIN SECB
KeywordsTRANSPORT PROTEIN / protein trasnport / translocation
Function / homology
Function and homology information


protein tetramerization / unfolded protein binding / protein transport / protein folding / cytoplasm
Similarity search - Function
Bacterial protein export chaperone SecB / Preprotein translocase subunit SecB / Bacterial Protein-export protein SecB / SecB-like / SecB-like superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Protein-export protein SecB
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsXu, Z. / Knafels, J.D. / Yoshino, K.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Crystal structure of the bacterial protein export chaperone secB.
Authors: Xu, Z. / Knafels, J.D. / Yoshino, K.
History
DepositionSep 25, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN-EXPORT PROTEIN SECB
B: PROTEIN-EXPORT PROTEIN SECB
C: PROTEIN-EXPORT PROTEIN SECB
D: PROTEIN-EXPORT PROTEIN SECB


Theoretical massNumber of molelcules
Total (without water)76,5854
Polymers76,5854
Non-polymers00
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6990 Å2
ΔGint-25 kcal/mol
Surface area25960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.344, 126.344, 148.333
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe biological assembly is a tetramer contained in the asymmetric unit

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Components

#1: Protein
PROTEIN-EXPORT PROTEIN SECB / SECB


Mass: 19146.301 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P44853
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.86 Å3/Da / Density % sol: 68.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Ammonium Sulfate, ethanol, PIPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
220 mMTris-HCl1drop
32.0 Mammonium sulfate1reservoir
410 %(v/v)ethanol1reservoir
5100 mMPIPES1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D
DetectorType: OTHER / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→45 Å / Num. obs: 42096 / % possible obs: 99.7 % / Redundancy: 12.3 % / Biso Wilson estimate: 46.5 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 20.3
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.292 / % possible all: 93.9
Reflection
*PLUS
Num. measured all: 515992
Reflection shell
*PLUS
% possible obs: 93.9 % / Mean I/σ(I) obs: 3.5

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.5→44.95 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 622143.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.301 4048 10.1 %RANDOM
Rwork0.241 ---
obs0.241 40192 95.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.21 Å2 / ksol: 0.354 e/Å3
Displacement parametersBiso mean: 59.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.21 Å20 Å20 Å2
2---2.21 Å20 Å2
3---4.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.5→44.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4422 0 0 63 4485
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it6.091.5
X-RAY DIFFRACTIONc_mcangle_it8.412
X-RAY DIFFRACTIONc_scbond_it8.732
X-RAY DIFFRACTIONc_scangle_it10.82.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.41 607 9.9 %
Rwork0.349 5511 -
obs--88.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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