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- PDB-3p04: Crystal Structure of the BCR protein from Corynebacterium glutami... -

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Basic information

Entry
Database: PDB / ID: 3p04
TitleCrystal Structure of the BCR protein from Corynebacterium glutamicum. Northeast Structural Genomics Consortium Target CgR8
ComponentsUncharacterized BCR
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / sepF homolog / DUF552 / PSI-Biology / NESG / Protein Structure Initiative / Northeast Structural Genomics Consortium / cell division / cytoplasma
Function / homology
Function and homology information


FtsZ-dependent cytokinesis / division septum assembly / cytoplasm
Similarity search - Function
Cell division protein SepF / SepF-like protein / Cell division protein SepF/SepF-related / SepF-like superfamily / Cell division protein SepF / Translation Initiation Factor IF3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Cell division protein SepF
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsVorobiev, S. / Lew, S. / Seetharaman, J. / Hamilton, H. / Xiao, R. / Patel, D.J. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. ...Vorobiev, S. / Lew, S. / Seetharaman, J. / Hamilton, H. / Xiao, R. / Patel, D.J. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the BCR protein from Corynebacterium glutamicum. Northeast Structural Genomics Consortium Target CgR8.
Authors: Vorobiev, S. / Lew, S. / Seetharaman, J. / Hamilton, H. / Xiao, R. / Patel, D.J. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionSep 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized BCR
B: Uncharacterized BCR


Theoretical massNumber of molelcules
Total (without water)19,7092
Polymers19,7092
Non-polymers00
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-11 kcal/mol
Surface area8550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.867, 57.885, 76.424
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 Uncharacterized BCR


Mass: 9854.664 Da / Num. of mol.: 2 / Fragment: sequence database residues 64-141 / Mutation: R120H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: cg2363, Cgl2152 / Plasmid: CgR8-64-141-21.27 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) +magic / References: UniProt: Q8NNN6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 1.96 Å3/Da / Density % sol: 37.13 %
Crystal growTemperature: 278 K / Method: microbatch under paraffin oil / pH: 5.1
Details: 20% PEG 3350, 0.2 M ammonium citrate, pH 5.1, Microbatch under Paraffin oil, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97899 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 21, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97899 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 15202 / Num. obs: 15202 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 18.7
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 5.9 / Num. unique all: 1516 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.6_289refinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→38.212 Å / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.243 702 4.64 %RANDOM
Rwork0.205 ---
obs0.207 15823 99.68 %-
Solvent computationShrinkage radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.188 Å2
Refinement stepCycle: LAST / Resolution: 2.2→38.212 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1133 0 0 91 1224
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_deg1.403
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_dihedral_angle_d16.334
Refinement TLS params.

S33: -0 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1810.04670.30420.2750.21940.1130.0242-0.0044-0.0563-0.0548-0.02780.0176-0.0356-0.01180.07270.0210.00480.0676-0.00080.077226.097333.329539.0424
20.1848-0.69840.1460.75410.02590.8367-0.04-0.06010.0093-0.0160.04140.02310.0540.00390.0297-0.01350.01070.0217-0.03150.000125.295425.135621.9482
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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