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- PDB-4mv7: Crystal Structure of Biotin Carboxylase form Haemophilus influenz... -

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Basic information

Entry
Database: PDB / ID: 4mv7
TitleCrystal Structure of Biotin Carboxylase form Haemophilus influenzae in Complex with Phosphonoformate
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
Dna Ligase; domain 1 - #20 / Dna Ligase; domain 1 / Acetyl-CoA carboxylase, biotin carboxylase / : / 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. ...Dna Ligase; domain 1 - #20 / Dna Ligase; domain 1 / Acetyl-CoA carboxylase, biotin carboxylase / : / 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 / Other non-globular / 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 / Special / Carbamoyl-phosphate synthase subdomain signature 2. / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHONOFORMIC ACID / Biotin carboxylase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 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)51,5974
Polymers51,3471
Non-polymers2503
Water3,549197
1
A: Biotin carboxylase
hetero molecules

A: Biotin carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,1938
Polymers102,6932
Non-polymers5006
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_345-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)86.006, 86.006, 103.135
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-666-

HOH

21A-791-

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-PPF / PHOSPHONOFORMIC ACID


Mass: 126.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH3O5P / Comment: medication, antivirus, inhibitor*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.14 Å3/Da / Density % sol: 42.64 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop
Details: 0.2M Sodium acetate trihydrate, 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: Dec 14, 2012 / 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: 1.73→43 Å / Num. all: 44317 / Num. obs: 44317 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 29.5 Å2 / Rsym value: 0.03 / Net I/σ(I): 19.9
Reflection shellResolution: 1.73→1.82 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 6492 / Rsym value: 0.41 / % possible all: 98.5

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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: 1.73→43 Å / SU ML: 0.17 / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.27 / Stereochemistry target values: ML / Details: Hydrogens have been added to the riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2034 2146 4.85 %Random
Rwork0.1751 ---
obs0.1765 44224 97.94 %-
all-44224 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.5 Å2
Refinement stepCycle: LAST / Resolution: 1.73→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3179 0 15 197 3391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093268
X-RAY DIFFRACTIONf_angle_d1.2524419
X-RAY DIFFRACTIONf_dihedral_angle_d14.4821227
X-RAY DIFFRACTIONf_chiral_restr0.069499
X-RAY DIFFRACTIONf_plane_restr0.006578
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.76980.26771400.27192785X-RAY DIFFRACTION98
1.7698-1.8140.28781500.24622784X-RAY DIFFRACTION98
1.814-1.86310.27471370.2312845X-RAY DIFFRACTION99
1.8631-1.91790.25591470.22792805X-RAY DIFFRACTION99
1.9179-1.97980.23141390.21192817X-RAY DIFFRACTION99
1.9798-2.05060.22911400.20072819X-RAY DIFFRACTION99
2.0506-2.13270.21941420.18682847X-RAY DIFFRACTION99
2.1327-2.22970.24441450.18692818X-RAY DIFFRACTION99
2.2297-2.34730.21631490.18042812X-RAY DIFFRACTION99
2.3473-2.49430.21191430.17832831X-RAY DIFFRACTION99
2.4943-2.68690.20641480.17272804X-RAY DIFFRACTION98
2.6869-2.95720.21311440.17792806X-RAY DIFFRACTION98
2.9572-3.3850.20661450.18262825X-RAY DIFFRACTION99
3.385-4.26410.19031430.15492727X-RAY DIFFRACTION95
4.2641-430.16221340.15212753X-RAY DIFFRACTION94
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)
13.4584-0.4451-0.35611.9994-0.44722.19350.03110.260.5082-0.09740.23760.4356-0.1779-0.4644-0.18570.21640.03570.01790.39320.15960.3627-81.1075-17.56221.968
25.8620.84170.3885.3525-0.46291.65820.69371.31450.4373-0.0092-0.6008-0.367-0.7391-0.020.15930.7438-0.00670.22950.8197-0.10710.7799-55.52934.938317.8397
33.1968-0.9115-0.81242.61570.47842.0755-0.0661-0.49040.65250.49690.3155-0.2675-0.08780.1227-0.08750.31170.0439-0.00070.2943-0.09050.2701-66.2845-18.875618.997
42.2894-0.8938-0.20163.3214-0.2521.64180.0160.21190.4144-0.22270.0364-0.60720.10790.1065-0.04250.2028-0.04350.05510.26550.03050.2976-55.8469-25.96470.5378
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 207 )
3X-RAY DIFFRACTION3chain 'A' and (resid 208 through 331 )
4X-RAY DIFFRACTION4chain 'A' and (resid 332 through 444 )

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