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- PDB-4mv8: Crystal Structure of Biotin Carboxylase from Haemophilus influenz... -

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Basic information

Entry
Database: PDB / ID: 4mv8
TitleCrystal Structure of Biotin Carboxylase from Haemophilus influenzae in Complex with AMPPCP 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / PHOSPHATE ION / Biotin carboxylase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 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
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)51,9473
Polymers51,3471
Non-polymers6002
Water1,838102
1
A: Biotin carboxylase
hetero molecules

A: Biotin carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,8936
Polymers102,6932
Non-polymers1,2004
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_365-x-2,-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)86.839, 86.839, 103.222
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-626-

HOH

21A-683-

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-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.19 Å3/Da / Density % sol: 43.79 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop
Details: 0.2M Sodium phosphate dibasic dihydrate, 20% PEG 3350, 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-C / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 4, 2013 / Details: KB mirrors
RadiationMonochromator: Cryogenically cooled double crystal Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.06→43.42 Å / Num. all: 27357 / Num. obs: 27357 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 43.9 Å2 / Rsym value: 0.03 / Net I/σ(I): 25.5
Reflection shellResolution: 2.06→2.17 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 3988 / Rsym value: 0.64 / % possible all: 99.8

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Processing

Software
NameVersionClassification
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: 2.06→43.42 Å / SU ML: 0.26 / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.95 / Stereochemistry target values: ML / Details: Hydrogens have been added to the riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2284 1338 4.91 %Random
Rwork0.1803 ---
obs0.1826 27255 99.66 %-
all-27255 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.1 Å2
Refinement stepCycle: LAST / Resolution: 2.06→43.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3323 0 36 102 3461
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033419
X-RAY DIFFRACTIONf_angle_d0.7444627
X-RAY DIFFRACTIONf_dihedral_angle_d15.0611292
X-RAY DIFFRACTIONf_chiral_restr0.044520
X-RAY DIFFRACTIONf_plane_restr0.003598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.1330.31631260.29642556X-RAY DIFFRACTION99
2.133-2.21840.30481390.26592570X-RAY DIFFRACTION99
2.2184-2.31940.27851340.24722579X-RAY DIFFRACTION100
2.3194-2.44160.31811320.23062579X-RAY DIFFRACTION100
2.4416-2.59460.29721320.21412591X-RAY DIFFRACTION100
2.5946-2.79490.26431370.2042594X-RAY DIFFRACTION100
2.7949-3.07610.26351310.20222593X-RAY DIFFRACTION100
3.0761-3.5210.22061370.18482589X-RAY DIFFRACTION100
3.521-4.43550.19931360.15052612X-RAY DIFFRACTION100
4.4355-43.420.19091340.14932654X-RAY DIFFRACTION100
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)
11.17770.43660.86071.578-0.30710.89750.1553-0.1452-0.52890.2630.1006-0.11590.6587-0.25150.02570.4668-0.0732-0.07820.4013-0.02640.4616-99.52613.4505-0.7945
20.1214-0.53740.07352.4368-0.37640.0599-0.29551.2145-0.47520.48720.2154-0.86050.12720.1476-0.14150.6393-0.31530.20641.0897-0.34461.2187-67.678223.0191-17.0369
30.39050.03040.00931.19840.0690.9552-0.22920.56120.0193-0.48810.3264-0.2918-0.01450.33920.06470.2809-0.14990.05940.7175-0.09660.3593-93.520827.2348-17.7161
41.44850.00460.52321.04610.64550.7894-0.1622-0.01880.37540.15670.2261-0.2127-0.18570.17170.14280.2474-0.0592-0.06570.5426-0.03240.4359-94.383139.56280.7816
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 116 )
2X-RAY DIFFRACTION2chain 'A' and (resid 117 through 206 )
3X-RAY DIFFRACTION3chain 'A' and (resid 207 through 331 )
4X-RAY DIFFRACTION4chain 'A' and (resid 332 through 445 )

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