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- PDB-5ikl: Crystal structure of P. aeruginosa geranyl-CoA carboxylase (GCC),... -

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Basic information

Entry
Database: PDB / ID: 5ikl
TitleCrystal structure of P. aeruginosa geranyl-CoA carboxylase (GCC), beta subunit
ComponentsGeranyl-CoA carboxylase, beta-subunit
KeywordsLIGASE / Carboxylase / organic acid metabolism
Function / homology
Function and homology information


geranoyl-CoA carboxylase activity / terpene catabolic process / methylcrotonoyl-CoA carboxylase complex / L-leucine catabolic process / fatty acid biosynthetic process
Similarity search - Function
Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Geranyl-CoA carboxylase, beta-subunit
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsHuang, C.S. / Jurado, A.R. / Tong, L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK067238 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM008281 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM008798 United States
CitationJournal: Nat Commun / Year: 2015
Title: Structure and substrate selectivity of the 750-kDa alpha6beta6 holoenzyme of geranyl-CoA carboxylase
Authors: Jurado, A.R. / Huang, C.S. / Zhang, X. / Zhou, Z.H. / Tong, L.
History
DepositionMar 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Geranyl-CoA carboxylase, beta-subunit
D: Geranyl-CoA carboxylase, beta-subunit
F: Geranyl-CoA carboxylase, beta-subunit


Theoretical massNumber of molelcules
Total (without water)171,7893
Polymers171,7893
Non-polymers00
Water43224
1
B: Geranyl-CoA carboxylase, beta-subunit
D: Geranyl-CoA carboxylase, beta-subunit
F: Geranyl-CoA carboxylase, beta-subunit

B: Geranyl-CoA carboxylase, beta-subunit
D: Geranyl-CoA carboxylase, beta-subunit
F: Geranyl-CoA carboxylase, beta-subunit


Theoretical massNumber of molelcules
Total (without water)343,5796
Polymers343,5796
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+5/61
Buried area38410 Å2
ΔGint-236 kcal/mol
Surface area100860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.722, 105.722, 550.760
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Geranyl-CoA carboxylase, beta-subunit


Mass: 57263.141 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria)
Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: atuC, PA2888 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HZV9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.59 Å3/Da / Density % sol: 52.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M Tris-HCl (pH 8.0), 60% (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 71918 / % possible obs: 98.6 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.084 / Χ2: 1.035 / Net I/av σ(I): 15.707 / Net I/σ(I): 11.7 / Num. measured all: 322453
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.4-2.494.50.43270291.04399.4
2.49-2.594.60.36271271.04399.8
2.59-2.74.60.28571421.02999.9
2.7-2.854.60.21371491.01100
2.85-3.024.60.16271820.96299.9
3.02-3.264.60.11371980.97599.8
3.26-3.584.60.08672300.97899.5
3.58-4.14.40.07272191.01698.5
4.1-5.174.20.06771881.13196.6
5.17-504.20.0574541.18193.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→47.195 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.898 / SU B: 9.963 / SU ML: 0.228 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.364 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2819 3660 5 %RANDOM
Rwork0.215 ---
obs0.2184 68848 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 201.29 Å2 / Biso mean: 65.984 Å2 / Biso min: 30.88 Å2
Baniso -1Baniso -2Baniso -3
1-1.82 Å20.91 Å2-0 Å2
2--1.82 Å20 Å2
3----5.91 Å2
Refinement stepCycle: final / Resolution: 2.4→47.195 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11122 0 0 24 11146
Biso mean---57.8 -
Num. residues----1486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01911314
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211039
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.97715300
X-RAY DIFFRACTIONr_angle_other_deg0.83325350
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.98151470
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.45123.907471
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.321151874
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9381585
X-RAY DIFFRACTIONr_chiral_restr0.0850.21714
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112967
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022492
X-RAY DIFFRACTIONr_mcbond_it4.8326.3725928
X-RAY DIFFRACTIONr_mcbond_other4.8316.3725927
X-RAY DIFFRACTIONr_mcangle_it7.0599.5347382
LS refinement shellResolution: 2.401→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 255 -
Rwork0.281 4938 -
all-5193 -
obs--99.1 %

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