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- PDB-2nx9: Crystal structure of the carboxyltransferase domain of the oxaloa... -

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Basic information

Entry
Database: PDB / ID: 2nx9
TitleCrystal structure of the carboxyltransferase domain of the oxaloacetate decarboxylase Na+ pump from Vibrio cholerae
ComponentsOxaloacetate decarboxylase 2, subunit alpha
KeywordsLYASE / oxaloacetate decarboxylase / carboxyltransferase structure / biotin enzymes / Zn2+ binding site / TIM-barrel fold
Function / homology
Function and homology information


oxaloacetate decarboxylase / methylmalonyl-CoA carboxytransferase / methylmalonyl-CoA carboxytransferase activity / oxaloacetate decarboxylase activity / sodium ion transport / metal ion binding
Similarity search - Function
Oxaloacetate decarboxylase, alpha subunit / Carboxylase, conserved domain / Conserved carboxylase domain / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase domain. / Biotin-binding site / Biotin-requiring enzymes attachment site. / Biotin-requiring enzyme / Biotinyl/lipoyl domain profile. ...Oxaloacetate decarboxylase, alpha subunit / Carboxylase, conserved domain / Conserved carboxylase domain / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase domain. / Biotin-binding site / Biotin-requiring enzymes attachment site. / Biotin-requiring enzyme / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Oxaloacetate decarboxylase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsStuder, R. / Dimroth, P.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structure of the Carboxyltransferase Domain of the Oxaloacetate Decarboxylase Na(+) Pump from Vibrio cholerae.
Authors: Studer, R. / Dahinden, P. / Wang, W.W. / Auchli, Y. / Li, X.D. / Dimroth, P.
History
DepositionNov 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 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_conn.ptnr2_label_seq_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: Oxaloacetate decarboxylase 2, subunit alpha
B: Oxaloacetate decarboxylase 2, subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,0924
Polymers102,9622
Non-polymers1312
Water9,710539
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-93 kcal/mol
Surface area34950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.825, 91.655, 116.422
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Oxaloacetate decarboxylase 2, subunit alpha


Mass: 51480.832 Da / Num. of mol.: 2 / Fragment: Carboxyltransferase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: O395-N1 / Gene: oadA-2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6A1F6, oxaloacetate decarboxylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 539 / 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: 2.35 Å3/Da / Density % sol: 47.72 %
Crystal growTemperature: 298 K / pH: 6.5
Details: 0.1 M Na-cacodylate 0.2 M (NH4)2SO4 5% glycerol 25% (w/v) PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.83301
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 20, 2005
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.83301 Å / Relative weight: 1
ReflectionResolution: 1.7→35 Å / Num. obs: 105661 / % possible obs: 98.5 % / Redundancy: 7.14 % / Biso Wilson estimate: 31.19 Å2 / Rmerge(I) obs: 0.123 / Rsym value: 0.104 / Net I/σ(I): 13.8
Reflection shellResolution: 1.7→35 Å / Redundancy: 5.82 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 2.47 / Rsym value: 0.809 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RQH

1rqh


Resolution: 1.7→35 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.92 / SU B: 10.271 / SU ML: 0.16 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.284 5272 5 %RANDOM
Rwork0.232 ---
obs0.235 100388 98.5 %-
all-100388 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.67 Å2
Baniso -1Baniso -2Baniso -3
1--2.13 Å20 Å20 Å2
2--0.1 Å20 Å2
3---2.03 Å2
Refinement stepCycle: LAST / Resolution: 1.7→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6994 0 2 539 7535
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227114
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4411.9659654
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7515906
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.83224.73315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.62151257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9971546
X-RAY DIFFRACTIONr_chiral_restr0.0930.21135
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025296
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.23601
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.24911
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2570
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.225
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1020.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.08424636
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.72437231
X-RAY DIFFRACTIONr_scbond_it4.6054.52787
X-RAY DIFFRACTIONr_scangle_it5.66862421
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 360 -
Rwork0.346 6774 -
obs--91.24 %
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)
12.078-0.17510.19950.8965-0.37550.288-0.0667-0.4841-0.1388-0.00480.0145-0.031-0.04750.0260.05220.01040.01790.00350.13970.0693-0.105-0.97217.130615.5066
22.7973-0.45170.4620.68-0.27040.7474-0.0325-0.0405-0.9181-0.41380.0019-0.06920.08750.08860.0306-0.00330.01110.0529-0.10820.12920.2762.8447-3.4596.2144
32.14880.02860.08040.7316-0.3620.8426-0.06740.20270.613-0.02040.04230.0374-0.01570.01710.02510.0175-0.001-0.0435-0.01340.10950.1035-2.88242.3348-10.1051
41.9529-0.12620.5020.26690.23361.8226-0.19640.01611.20330.00470.0507-0.1931-0.2610.14280.1457-0.0111-0.0705-0.062-0.11470.12150.705411.434259.7473-5.6965
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 3054 - 305
2X-RAY DIFFRACTION2AA306 - 454306 - 454
3X-RAY DIFFRACTION3BB2 - 3062 - 306
4X-RAY DIFFRACTION4BB307 - 454307 - 454

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