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- PDB-4rzq: Structural Analysis of Substrate, Reaction Intermediate and Produ... -

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Basic information

Entry
Database: PDB / ID: 4rzq
TitleStructural Analysis of Substrate, Reaction Intermediate and Product Binding in Haemophilus influenzae Biotin Carboxylase
ComponentsBiotin carboxylase
KeywordsLIGASE / ATP Grasp / Carboxylase / Biotin Carboxyl Carrier Protein and Carboxyltransferase
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. / Biotin carboxylase C-terminal domain ...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 / Rudiment single hybrid motif / Other non-globular / 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 / Special / Carbamoyl-phosphate synthase subdomain signature 2. / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-Y7Y / Biotin carboxylase
Similarity search - Component
Biological speciesHaemophilus influenzae Rd KW20 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsBroussard, T.C. / Pakhomova, S. / Neau, D.B. / Champion, T.S. / Bonnot, R. / 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
DepositionDec 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2015Group: Database references
Revision 1.2Sep 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)52,0903
Polymers51,3471
Non-polymers7442
Water1,51384
1
A: Biotin carboxylase
hetero molecules

A: Biotin carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,1806
Polymers102,6932
Non-polymers1,4874
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)86.197, 86.197, 102.364
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-648-

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 Rd KW20 (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-Y7Y / methyl (3aS,4S,6aR)-4-(5-methoxy-5-oxopentyl)-2-oxohexahydro-1H-thieno[3,4-d]imidazole-1-carboxylate


Mass: 316.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H20N2O5S
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 42.47 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop
Details: 16% PEG3350 0.2M KCl Protein was incubated with solid N1 -methoxycarbonylbiotin methyl ester for 5 days prior to crystallization, VAPOR DIFFUSION, SITTING DROP, temperature 298.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 31, 2013 / Details: KB MIRRORS
RadiationMonochromator: CRYOGENICALLY-COOLED SINGLE CRYSTAL SI(220) SIDE BOUNCE
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.98→39.72 Å / Num. all: 30073 / Num. obs: 30073 / % possible obs: 99.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 27.7 Å2 / Rsym value: 0.056 / Net I/σ(I): 19.5
Reflection shellResolution: 1.98→2.09 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 4385 / Rsym value: 0.504 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata scaling
MOLREPphasing
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DV1

1dv1


Resolution: 1.98→39.72 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 8.307 / SU ML: 0.116 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21697 1464 4.9 %RANDOM
Rwork0.17629 ---
all0.17828 28578 --
obs0.17828 28578 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.666 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0.05 Å20 Å2
2---0.11 Å2-0 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.98→39.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3235 0 48 84 3367
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193365
X-RAY DIFFRACTIONr_bond_other_d0.0010.023259
X-RAY DIFFRACTIONr_angle_refined_deg2.0551.9794556
X-RAY DIFFRACTIONr_angle_other_deg0.9133.0027506
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7975422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.75323.862145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.19715573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.181524
X-RAY DIFFRACTIONr_chiral_restr0.1160.2513
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213757
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02728
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6881.6971691
X-RAY DIFFRACTIONr_mcbond_other1.6821.6941690
X-RAY DIFFRACTIONr_mcangle_it2.4682.5322109
X-RAY DIFFRACTIONr_mcangle_other2.4672.5362110
X-RAY DIFFRACTIONr_scbond_it2.7252.0521674
X-RAY DIFFRACTIONr_scbond_other2.7242.0551675
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.793.0152447
X-RAY DIFFRACTIONr_long_range_B_refined5.60114.5563713
X-RAY DIFFRACTIONr_long_range_B_other5.60114.5713714
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.98→2.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 95 -
Rwork0.239 2123 -
obs-2123 100 %
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)
13.71170.32410.56693.1056-0.50021.90610.0637-0.0246-0.1841-0.28320.07220.53620.2353-0.3762-0.13590.1633-0.0796-0.11310.10520.03990.138218.631-5.503-7.711
23.3913-4.0648-1.04095.37931.39340.3923-0.417-0.12710.12520.22260.36390.3805-0.06250.02620.05310.6768-0.01450.0230.80740.05480.857610.23426.3539.399
32.93211.273-0.53053.14520.03151.60990.2038-0.65830.44680.3507-0.05260.3656-0.1324-0.2153-0.15110.1095-0.01010.03810.26-0.05860.089927.0967.9589.583
43.8384-1.07022.8011.7813-1.53313.3412-0.02660.4890.4458-0.429-0.057-0.0162-0.060.17010.08350.21520.00950.0170.09440.09260.098334.8517.844-15.429
52.986-0.2637-0.16182.92380.10863.42930.0811-0.01610.7117-0.20150.0074-0.0116-0.30750.0285-0.08860.1012-0.00920.01980.02830.00880.177439.71716.97-4.255
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 109
2X-RAY DIFFRACTION2A110 - 206
3X-RAY DIFFRACTION3A207 - 338
4X-RAY DIFFRACTION4A339 - 382
5X-RAY DIFFRACTION5A383 - 444

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