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- PDB-2evb: Structure of Biotin Carboxyl Carrier Protein (74Val start) from P... -

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Basic information

Entry
Database: PDB / ID: 2evb
TitleStructure of Biotin Carboxyl Carrier Protein (74Val start) from Pyrococcus horikoshi OT3 Ligand Free Form I
Componentsmethylmalonyl-CoA decarboxylase gamma chain
KeywordsLIPID BINDING PROTEIN / TRANSFERASE / Biotin / BCCP / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


: / Biotin-binding site / Biotin-requiring enzymes attachment site. / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Biotin-requiring enzyme / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
149aa long hypothetical methylmalonyl-CoA decarboxylase gamma chain
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsBagautdinov, B. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Protein biotinylation visualized by a complex structure of biotin protein ligase with a substrate
Authors: Bagautdinov, B. / Matsuura, Y. / Bagautdinova, S. / Kunishima, N.
History
DepositionOct 31, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 1, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: methylmalonyl-CoA decarboxylase gamma chain


Theoretical massNumber of molelcules
Total (without water)7,9851
Polymers7,9851
Non-polymers00
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.064, 39.537, 57.695
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 methylmalonyl-CoA decarboxylase gamma chain / Biotin Carboxyl Carrier Protein


Mass: 7985.457 Da / Num. of mol.: 1 / Fragment: residues 73-146
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: bccp / Plasmid: PET 11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O59021, methylmalonyl-CoA carboxytransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 1.931508 Å3/Da / Density % sol: 36.319191 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 4.62
Details: PEG 550 MME 55w/v(%), Acetate, NaOH , pH 4.62, microbatch, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 2, 2005 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→24.5 Å / Num. all: 8858 / Num. obs: 8821 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 23.82 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.05 / Net I/σ(I): 22.3
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 0.165 / Num. unique all: 560 / % possible all: 62.2

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BDO

1bdo


Resolution: 1.55→24.5 Å / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.283 469 -RANDOM
Rwork0.248 ---
obs0.248 8821 93.5 %-
all-8858 --
Displacement parametersBiso mean: 30.2 Å2
Baniso -1Baniso -2Baniso -3
1-6.45 Å20 Å20 Å2
2---8.24 Å20 Å2
3---1.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.55→24.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms556 0 0 111 667
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.5
X-RAY DIFFRACTIONc_improper_angle_d0.95
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
1.55-1.610.326280.3220.06256061.2
1.61-1.670.397440.340.0685391.6

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