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- PDB-2vr1: Crystal structure of Biotin carboxylase from E. coli in complex w... -

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Basic information

Entry
Database: PDB / ID: 2vr1
TitleCrystal structure of Biotin carboxylase from E. coli in complex with ATP analog, ADPCF2P.
ComponentsBIOTIN CARBOXYLASE
KeywordsLIGASE / NUCLEOTIDE-BINDING / FATTY ACID BIOSYNTHESIS / LIPID SYNTHESIS / BIOTIN CARBOXYLASE / FAS / BIOTIN / BACTERIAL / ATP-BINDING
Function / homology
Function and homology information


biotin carboxylase / acetyl-CoA carboxylase complex / biotin carboxylase activity / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / negative regulation of fatty acid biosynthetic process / fatty acid biosynthetic process / protein homodimerization activity / ATP binding / metal ion binding ...biotin carboxylase / acetyl-CoA carboxylase complex / biotin carboxylase activity / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / negative regulation of fatty acid biosynthetic process / fatty acid biosynthetic process / protein homodimerization activity / ATP binding / metal ion binding / cytoplasm / cytosol
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
Chem-ATF / Biotin carboxylase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMochalkin, I. / Waldrop, G.L.
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 24, 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 / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)99,3855
Polymers98,7732
Non-polymers6123
Water4,197233
1
A: BIOTIN CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9633
Polymers49,3871
Non-polymers5772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: BIOTIN CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4222
Polymers49,3871
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)84.129, 106.784, 121.910
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 BIOTIN CARBOXYLASE / ACETYL-COA CARBOXYLASE SUBUNIT A / ACC


Mass: 49386.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P24182, biotin carboxylase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ATF / PHOSPHODIFLUOROMETHYLPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 541.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16F2N5O12P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.78 Å3/Da / Density % sol: 55.46 % / Description: NONE
Crystal growDetails: 0.1M KCL, 3-8% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorDate: May 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 32843 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.83
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.3 / % possible all: 96.7

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Processing

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

1dv2


Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.901 / SU B: 20.689 / SU ML: 0.222 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.773 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1668 5.1 %RANDOM
Rwork0.189 ---
obs0.192 31155 95.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å20 Å20 Å2
2--2.37 Å20 Å2
3----1.41 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6755 0 35 233 7023
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226916
X-RAY DIFFRACTIONr_bond_other_d0.0030.026429
X-RAY DIFFRACTIONr_angle_refined_deg1.1111.9729345
X-RAY DIFFRACTIONr_angle_other_deg0.741314930
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3345869
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65323.666311
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.294151210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3881557
X-RAY DIFFRACTIONr_chiral_restr0.0620.21034
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027698
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021371
X-RAY DIFFRACTIONr_nbd_refined0.190.21376
X-RAY DIFFRACTIONr_nbd_other0.1720.26345
X-RAY DIFFRACTIONr_nbtor_refined0.1720.23338
X-RAY DIFFRACTIONr_nbtor_other0.0780.24237
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2198
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1220.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1630.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0740.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5091.55645
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.56526960
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.89532950
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.3914.52385
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: 2.6→2.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.312 113
Rwork0.252 2192
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)
10.62140.2496-0.03610.89740.04770.68750.0005-0.0151-0.0174-0.05260.03090.11550.0183-0.0295-0.0315-0.06010.0257-0.0252-0.0589-0.0109-0.051718.9183-19.880224.691
20.9808-0.4924-0.52481.4167-0.22591.5044-0.0744-0.18390.00780.10970.0484-0.15840.03790.26450.0259-0.1146-0.0155-0.0305-0.0445-0.0265-0.078142.5416-0.283854.2956
3100.968336.791428.530771.186417.23368.8711-0.10680.53561.129-2.9986-0.9962-4.3198-3.21940.19321.103-0.0036-0.0027-0.0039-0.00120.00010.00037.1463-23.135822.8207
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 446
2X-RAY DIFFRACTION2B1 - 446
3X-RAY DIFFRACTION3A1448

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