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- PDB-2c00: Crystal Structure of Biotin Carboxylase from Pseudomonas aerugino... -

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Basic information

Entry
Database: PDB / ID: 2c00
TitleCrystal Structure of Biotin Carboxylase from Pseudomonas aeruginosa in apo form
ComponentsBIOTIN CARBOXYLASE
KeywordsLIGASE / NUCLEOTIDE-BINDING / FATTY ACID BIOSYNTHESIS / ATP-GRASP DOMAIN / BIOTIN CARBOXYLASE / BIOTIN / ATP-BINDING / LIPID SYNTHESIS
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 / ATP-grasp fold, A domain / Rudiment single hybrid motif / 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
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 21, 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 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BIOTIN CARBOXYLASE
B: BIOTIN CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,7524
Polymers101,5592
Non-polymers1922
Water8,791488
1
A: BIOTIN CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8762
Polymers50,7801
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: BIOTIN CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8762
Polymers50,7801
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)160.402, 160.402, 146.764
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 50779.715 Da / Num. of mol.: 2
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 488 / Source method: isolated from a natural source / Formula: H2O
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: 5.37 Å3/Da / Density % sol: 76.93 % / Description: NONE
Crystal growDetails: 0.1M TRIS (PH 7.0); 0.2M MGCL2; 17-21% 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 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 75554 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 33.6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 4.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DV1

1dv1


Resolution: 2.5→46.13 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.934 / SU B: 9.635 / SU ML: 0.116 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.223 3769 5 %RANDOM
Rwork0.196 ---
obs0.198 71168 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20.26 Å20 Å2
2--0.52 Å20 Å2
3----0.77 Å2
Refinement stepCycle: LAST / Resolution: 2.5→46.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6731 0 10 488 7229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226873
X-RAY DIFFRACTIONr_bond_other_d0.0010.024720
X-RAY DIFFRACTIONr_angle_refined_deg1.0831.9729288
X-RAY DIFFRACTIONr_angle_other_deg0.842311498
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8115877
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59323.734308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.867151189
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1581557
X-RAY DIFFRACTIONr_chiral_restr0.0690.21041
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027707
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021354
X-RAY DIFFRACTIONr_nbd_refined0.1990.21237
X-RAY DIFFRACTIONr_nbd_other0.190.24738
X-RAY DIFFRACTIONr_nbtor_refined0.1680.23310
X-RAY DIFFRACTIONr_nbtor_other0.0810.23725
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2348
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0910.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2240.217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7231.55684
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.78627005
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.19532833
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.84.52283
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: 2.5→2.57 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.345 289
Rwork0.301 5189
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)
10.6312-0.31920.04110.85160.2321.8344-0.066-0.02120.09330.01140.0245-0.0658-0.1094-0.1260.0415-0.0937-0.0407-0.0328-0.06950.0074-0.053-76.169642.39812.4376
20.45040.48690.0922.28080.07360.0192-0.0437-0.0709-0.21540.28470.0265-0.35240.23250.03020.01720.14850.0343-0.0249-0.09910.0631-0.0108-65.85661.211112.3108
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 445
2X-RAY DIFFRACTION2B1 - 445

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