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- PDB-2vpq: Crystal structure of biotin carboxylase from S. aureus complexed ... -

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Basic information

Entry
Database: PDB / ID: 2vpq
TitleCrystal structure of biotin carboxylase from S. aureus complexed with AMPPNP
ComponentsACETYL-COA CARBOXYLASE
KeywordsLIGASE / BACTERIA / ATP-GRASP DOMAIN / BIOTIN CARBOXYLASE
Function / homology
Function and homology information


acetyl-CoA carboxylase / biotin carboxylase / biotin carboxylase activity / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / fatty acid biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
Acetyl-CoA carboxylase, biotin carboxylase / : / Rossmann fold - #20 / Biotin carboxylase-like, N-terminal domain / Biotin carboxylase, C-terminal / Biotin carboxylation domain / Biotin carboxylase, N-terminal domain / Biotin carboxylase C-terminal domain / Biotin carboxylation domain profile. / Biotin carboxylase C-terminal domain ...Acetyl-CoA carboxylase, biotin carboxylase / : / Rossmann fold - #20 / Biotin carboxylase-like, N-terminal domain / Biotin carboxylase, C-terminal / Biotin carboxylation domain / Biotin carboxylase, N-terminal domain / Biotin carboxylase C-terminal domain / Biotin carboxylation domain profile. / Biotin carboxylase C-terminal domain / Carbamoyl-phosphate synthase subdomain signature 1. / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / ATP-grasp fold, A domain / Rudiment single hybrid motif / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold, B domain / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Carbamoyl-phosphate synthase subdomain signature 2. / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Biotin carboxylase / Biotin carboxylase
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMochalkin, I.
CitationJournal: Protein Sci. / Year: 2008
Title: Structural Evidence for Substrate-Induced Synergism and Half-Sites Reactivity in Biotin Carboxylase.
Authors: Mochalkin, I. / Miller, J.R. / Evdokimov, A. / Lightle, S. / Yan, C. / Stover, C.K. / Waldrop, G.L.
History
DepositionMar 3, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACETYL-COA CARBOXYLASE
B: ACETYL-COA CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,39310
Polymers100,2122
Non-polymers1,1818
Water14,718817
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-16 kcal/mol
Surface area41230 Å2
MethodPQS
Unit cell
Length a, b, c (Å)78.247, 63.318, 105.142
Angle α, β, γ (deg.)90.00, 103.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ACETYL-COA CARBOXYLASE / BIOTIN CARBOXYLASE


Mass: 50106.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q99TW7, UniProt: A0A0H3JRR2*PLUS, biotin carboxylase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 817 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER (ANP): ATP ANALOG

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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: 2.29 Å3/Da / Density % sol: 45.96 % / Description: NONE
Crystal growDetails: 0.2M KCL; 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 13, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 55214 / % possible obs: 93.8 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.07
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.9 / % possible all: 70.1

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
REFMACphasing
REFMAC5.2.0019refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DV2

1dv2


Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.878 / SU B: 14.212 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.289 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.284 2810 5.1 %RANDOM
Rwork0.215 ---
obs0.219 52269 94.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å2-0.21 Å2
2---1.68 Å20 Å2
3---1.23 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6967 0 68 817 7852
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0227184
X-RAY DIFFRACTIONr_bond_other_d0.0010.024887
X-RAY DIFFRACTIONr_angle_refined_deg1.2311.9789719
X-RAY DIFFRACTIONr_angle_other_deg0.885311957
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0095899
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.81124.788330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.201151274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6231542
X-RAY DIFFRACTIONr_chiral_restr0.070.21075
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027997
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021395
X-RAY DIFFRACTIONr_nbd_refined0.1940.21561
X-RAY DIFFRACTIONr_nbd_other0.1920.25333
X-RAY DIFFRACTIONr_nbtor_refined0.1710.23508
X-RAY DIFFRACTIONr_nbtor_other0.0840.23825
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2617
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2460.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6081.55823
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.70727179
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.18133137
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.794.52538
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.336 161
Rwork0.272 2822

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