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- PDB-2vqd: Crystal Structure of Biotin Carboxylase from Pseudomonas aerugino... -

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Basic information

Entry
Database: PDB / ID: 2vqd
TitleCrystal Structure of Biotin Carboxylase from Pseudomonas aeruginosa complexed with AMPCP
ComponentsBIOTIN CARBOXYLASE
KeywordsLIGASE / NUCLEOTIDE-BINDING / FATTY ACID BIOSYNTHESIS / LIPID SYNTHESIS / ATP-GRASP DOMAIN / BIOTIN CARBOXYLASE / BIOTIN / BACTERIA / ATP-BINDING
Function / homology
Function and homology information


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 / Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain / 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 / Rossmann fold - #20 ...Acetyl-CoA carboxylase, biotin carboxylase / Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain / 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 / Rossmann fold - #20 / Carbamoyl-phosphate synthase subdomain signature 1. / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Rudiment single hybrid motif / ATP-grasp fold, A domain / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / Biotin carboxylase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.41 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 13, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
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.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.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: BIOTIN CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3254
Polymers50,7801
Non-polymers5463
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)64.227, 126.786, 49.878
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2176-

HOH

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Components

#1: Protein BIOTIN CARBOXYLASE / / ACETYL-COA CARBOXYLASE SUBUNIT A / ACC


Mass: 50779.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P37798, biotin carboxylase
#2: Chemical ChemComp-AP2 / PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER


Mass: 425.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17N5O9P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER (AP2): NON-HYDROLYZABLE ADP ANALOG
Sequence detailsC-TERMINAL HIS-TAG PRESENT

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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: 1.97 Å3/Da / Density % sol: 37.02 % / Description: NONE
Crystal growDetails: 0.1M HEPES (PH 7.0), 0.2M MGCL2, 15-20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.54
DetectorDate: May 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 15777 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 22.9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.86 / % possible all: 83.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DV2

1dv2


Resolution: 2.41→63.37 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.916 / SU B: 18.358 / SU ML: 0.229 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.859 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.252 791 5 %RANDOM
Rwork0.178 ---
obs0.182 14953 95.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.49 Å2
Baniso -1Baniso -2Baniso -3
1-1.51 Å20 Å20 Å2
2--0.21 Å20 Å2
3----1.73 Å2
Refinement stepCycle: LAST / Resolution: 2.41→63.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3412 0 33 232 3677
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223514
X-RAY DIFFRACTIONr_bond_other_d0.0010.023247
X-RAY DIFFRACTIONr_angle_refined_deg1.2121.9814756
X-RAY DIFFRACTIONr_angle_other_deg0.75837541
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8535448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.8523.718156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.60415600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9111529
X-RAY DIFFRACTIONr_chiral_restr0.0650.2529
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023943
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02697
X-RAY DIFFRACTIONr_nbd_refined0.1880.2691
X-RAY DIFFRACTIONr_nbd_other0.1760.23225
X-RAY DIFFRACTIONr_nbtor_refined0.1650.21687
X-RAY DIFFRACTIONr_nbtor_other0.0820.22141
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2176
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1820.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5431.52883
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.61923558
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.02131469
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.5034.51198
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: 2.41→2.47 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.321 44
Rwork0.224 884
Refinement TLS params.

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 °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.59960.0165-0.14971.9352-0.39720.35160.03930.01070.08270.211-0.042-0.114-0.0783-0.00120.0027-0.0552-0.0093-0.0309-0.0555-0.017-0.09936.121920.344913.0923
219.7093-0.360517.168730.05040.822814.99860.6192-0.51990.7931-0.1356-0.80251.4562-0.24690.40230.18330.0057-0.0160.00670.0004-0.00960.00310.335831.08489.8703
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 447
2X-RAY DIFFRACTION2A1448

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