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- PDB-4mv4: Crystal Structure of Biotin Carboxylase from Haemophilus influenz... -

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Basic information

Entry
Database: PDB / ID: 4mv4
TitleCrystal Structure of Biotin Carboxylase from Haemophilus influenzae in Complex with AMPPCP and Mg2
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, 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Biotin carboxylase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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)52,0366
Polymers51,3471
Non-polymers6895
Water5,441302
1
A: Biotin carboxylase
hetero molecules

A: Biotin carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,07112
Polymers102,6932
Non-polymers1,37810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_685-x+1,-y+3,z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.344, 85.344, 104.217
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-651-

HOH

21A-877-

HOH

31A-887-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 307 molecules

#2: 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
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 42.36 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop
Details: 0.2M NaCl, 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: 1.61→42.6 Å / Num. all: 54685 / Num. obs: 54685 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Biso Wilson estimate: 21.8 Å2 / Rsym value: 0.03 / Net I/σ(I): 17.2
Reflection shellResolution: 1.61→1.7 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 7993 / Rsym value: 0.32 / % possible all: 99

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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: 1.61→42.6 Å / SU ML: 0.15 / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.2 / Stereochemistry target values: ML / Details: Hydrogens have been added to the riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1843 2721 4.98 %Random
Rwork0.1542 ---
obs0.1557 54662 98.24 %-
all-54662 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.7 Å2
Refinement stepCycle: LAST / Resolution: 1.61→42.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3394 0 41 302 3737
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.023538
X-RAY DIFFRACTIONf_angle_d1.4144791
X-RAY DIFFRACTIONf_dihedral_angle_d14.7991342
X-RAY DIFFRACTIONf_chiral_restr0.082533
X-RAY DIFFRACTIONf_plane_restr0.008624
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.6390.25511400.23282737X-RAY DIFFRACTION99
1.639-1.67050.26091630.21382719X-RAY DIFFRACTION99
1.6705-1.70460.22991500.20542753X-RAY DIFFRACTION99
1.7046-1.74170.27751390.19522738X-RAY DIFFRACTION99
1.7417-1.78220.21571480.17812722X-RAY DIFFRACTION99
1.7822-1.82680.20651490.17372717X-RAY DIFFRACTION98
1.8268-1.87620.22181370.16772743X-RAY DIFFRACTION99
1.8762-1.93140.20641390.17432769X-RAY DIFFRACTION99
1.9314-1.99370.21941420.16652748X-RAY DIFFRACTION99
1.9937-2.0650.19031410.16392756X-RAY DIFFRACTION99
2.065-2.14770.19271320.15632755X-RAY DIFFRACTION98
2.1477-2.24540.18751470.15062746X-RAY DIFFRACTION99
2.2454-2.36380.18791370.1442744X-RAY DIFFRACTION99
2.3638-2.51190.19351480.15032754X-RAY DIFFRACTION99
2.5119-2.70580.19561410.14782715X-RAY DIFFRACTION98
2.7058-2.9780.17471410.16152732X-RAY DIFFRACTION98
2.978-3.40880.18511520.16242772X-RAY DIFFRACTION99
3.4088-4.2940.16261380.13572658X-RAY DIFFRACTION95
4.294-42.60.14891370.13512663X-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)
12.54010.76910.23971.7491-0.41961.36810.0712-0.2337-0.3271-0.00110.09840.33550.0733-0.1507-0.1150.1556-0.0285-0.04820.19650.06730.2534-37.72990.7539-8.3179
21.92840.39420.36291.65-0.45630.97720.2244-0.3644-0.5437-0.4961-0.16850.17230.4087-0.19250.18480.38060.0328-0.120.3191-0.07060.4542-14.893467.3528-22.0475
32.5602-0.07750.0621.1750.0770.96630.1170.4167-0.3432-0.3867-0.02450.02480.12630.0556-0.0850.27220.0143-0.04220.1861-0.03150.1484-22.702592.5812-24.7874
41.87750.08790.21341.9207-0.13971.47840.0526-0.1559-0.04470.074-0.0433-0.3279-0.04530.1046-0.00380.1466-0.0071-0.02840.1510.02640.1727-12.626999.6362-6.0696
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 445 )

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