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- PDB-5gu8: Structure of biotin carboxyl carrier protein from pyrococcus hori... -

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Basic information

Entry
Database: PDB / ID: 5gu8
TitleStructure of biotin carboxyl carrier protein from pyrococcus horikoshi OT3 (delta N79) wild type
Components149aa long hypothetical methylmalonyl-CoA decarboxylase gamma chain
KeywordsTRANSFERASE / Surface engineering / Crystal packing / Crystal contact engineering
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: 1.8 Å
AuthorsYamada, K. / Kunishima, N. / Matsuura, Y. / Nakai, K. / Naitow, H. / Fukasawa, Y. / Tomii, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)Platform Project for Supporting in Drug Discovery and Life Science Research Japan
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Designing better diffracting crystals of biotin carboxyl carrier protein from Pyrococcus horikoshii by a mutation based on the crystal-packing propensity of amino acids.
Authors: Yamada, K.D. / Kunishima, N. / Matsuura, Y. / Nakai, K. / Naitow, H. / Fukasawa, Y. / Tomii, K.
History
DepositionAug 26, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 149aa long hypothetical methylmalonyl-CoA decarboxylase gamma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7232
Polymers7,7001
Non-polymers231
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.861, 39.954, 59.641
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 149aa long hypothetical methylmalonyl-CoA decarboxylase gamma chain


Mass: 7700.118 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 80-149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: PH1284 / Plasmid: PET 11A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O59021
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.08 Å3/Da / Density % sol: 40.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 3.5 M sodium formate, 0.1 M Tris buffer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→33.2 Å / Num. obs: 6329 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 11.3 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 30.5
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 11.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EVB

2evb


Resolution: 1.8→33.2 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / Phase error: 17.34
RfactorNum. reflection% reflectionSelection details
Rfree0.1967 319 5.04 %Random
Rwork0.1601 ---
obs0.162 6329 100 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 16.9 Å2
Refinement stepCycle: LAST / Resolution: 1.8→33.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms536 0 1 86 623
LS refinement shellResolution: 1.8→2.27 Å
RfactorNum. reflection% reflection
Rfree0.1949 156 5.06 %
Rwork0.1539 2924 -
obs--100 %

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