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- PDB-4mv1: Crystal Structure of Biotin Carboxylase from Haemophilus influenz... -

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Basic information

Entry
Database: PDB / ID: 4mv1
TitleCrystal Structure of Biotin Carboxylase from Haemophilus influenzae in Complex with ADP and Phosphate
ComponentsBiotin carboxylase
KeywordsLIGASE / ATP-grasp
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 / : / 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
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Biotin carboxylase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsBroussard, T.C. / Pakhomova, S. / Neau, D.B. / Champion, T.S. / Bonnot, R.J. / Waldrop, G.L.
CitationJournal: Biochemistry / Year: 2015
Title: Structural Analysis of Substrate, Reaction Intermediate, and Product Binding in Haemophilus influenzae Biotin Carboxylase.
Authors: Broussard, T.C. / Pakhomova, S. / Neau, D.B. / Bonnot, R. / Waldrop, G.L.
History
DepositionSep 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Sep 20, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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)51,9935
Polymers51,3471
Non-polymers6464
Water3,459192
1
A: Biotin carboxylase
hetero molecules

A: Biotin carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,98610
Polymers102,6932
Non-polymers1,2938
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.733, 85.733, 103.042
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11A-632-

HOH

21A-769-

HOH

31A-792-

HOH

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Components

#1: Protein Biotin carboxylase / Acetyl-CoA carboxylase subunit A / ACC


Mass: 51346.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: accC, HI_0972 / Production host: Escherichia coli (E. coli)
References: UniProt: P43873, biotin carboxylase, acetyl-CoA carboxylase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.13 Å3/Da / Density % sol: 42.23 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M MES monohydrate (pH 6.0), 20% PEGMME 2000, VAPOR DIFFUSION, SITTING DROP, temperature 295.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2012 / Details: KB mirrors
RadiationMonochromator: Cryogenically cooled single crystal Si (311) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.91→42.33 Å / Num. all: 33103 / Num. obs: 33103 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 29.4 Å2 / Rsym value: 0.05 / Net I/σ(I): 18.3
Reflection shellResolution: 1.91→2.01 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 4827 / Rsym value: 0.62 / % possible all: 99.9

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Processing

Software
NameVersionClassification
Adxvdata processing
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1DV1

1dv1


Resolution: 1.91→31.173 Å / SU ML: 0.21 / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.59 / Stereochemistry target values: ML / Details: Hydrogens have been added to the riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2007 1615 4.9 %Random
Rwork0.1654 ---
obs0.1671 32942 98.84 %-
all-33103 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.8 Å2
Refinement stepCycle: LAST / Resolution: 1.91→31.173 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3317 0 40 192 3549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093427
X-RAY DIFFRACTIONf_angle_d1.2854635
X-RAY DIFFRACTIONf_dihedral_angle_d15.1811292
X-RAY DIFFRACTIONf_chiral_restr0.068521
X-RAY DIFFRACTIONf_plane_restr0.005600
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.96580.35861310.292573X-RAY DIFFRACTION98
1.9658-2.02930.27541300.23972653X-RAY DIFFRACTION99
2.0293-2.10180.271310.21682598X-RAY DIFFRACTION99
2.1018-2.18590.28141350.19592605X-RAY DIFFRACTION99
2.1859-2.28540.26221320.18742588X-RAY DIFFRACTION99
2.2854-2.40580.23891360.17122607X-RAY DIFFRACTION99
2.4058-2.55650.2151350.16872628X-RAY DIFFRACTION99
2.5565-2.75380.21631420.16532615X-RAY DIFFRACTION99
2.7538-3.03070.23891370.17042632X-RAY DIFFRACTION99
3.0307-3.46870.19531390.17012606X-RAY DIFFRACTION99
3.4687-4.36830.15991370.13772638X-RAY DIFFRACTION99
4.3683-31.1730.1421300.13912584X-RAY DIFFRACTION96
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)
15.0194-0.90970.35213.23180.2752.40540.19310.5178-0.6564-0.05260.0913-0.59010.1480.4551-0.09580.24060.0703-0.08520.2959-0.14880.3733-4.896217.302-22.4094
26.41782.44320.00775.9629-0.67071.67480.35641.1115-0.56450.2596-0.18190.13450.4166-0.0971-0.21680.5361-0.0107-0.17950.59660.05550.6882-28.6591-6.0736-7.4841
33.6506-0.71670.63723.1186-0.46331.77360.0601-0.6259-0.62010.8230.16120.20860.1203-0.1444-0.10440.48380.0008-0.02080.27550.08240.2467-19.848518.8188-5.6716
43.3488-1.09370.56973.67180.23362.08920.13990.3433-0.4603-0.1112-0.04590.72960.0023-0.1382-0.00710.2115-0.0153-0.04660.2111-0.04510.3247-30.105925.9546-24.1018
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:116)A1 - 116
2X-RAY DIFFRACTION2(CHAIN A AND RESID 117:207)A117 - 207
3X-RAY DIFFRACTION3(CHAIN A AND RESID 208:331)A208 - 331
4X-RAY DIFFRACTION4(CHAIN A AND RESID 332:444)A332 - 444

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