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- PDB-3hbl: Crystal Structure of S. aureus Pyruvate Carboxylase T908A Mutant -

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Basic information

Entry
Database: PDB / ID: 3hbl
TitleCrystal Structure of S. aureus Pyruvate Carboxylase T908A Mutant
ComponentsPyruvate carboxylase
KeywordsLIGASE / TIM barrel / Pyruvate
Function / homology
Function and homology information


pyruvate carboxylase / pyruvate carboxylase activity / pyruvate metabolic process / gluconeogenesis / ATP binding / identical protein binding / metal ion binding
Similarity search - Function
Arc Repressor Mutant, subunit A - #2790 / pyruvate carboxylase f1077a mutant fold / pyruvate carboxylase f1077a mutant domain / Conserved carboxylase domain / Pyruvate carboxylase / Carboxylase, conserved domain / Conserved carboxylase domain / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase domain. ...Arc Repressor Mutant, subunit A - #2790 / pyruvate carboxylase f1077a mutant fold / pyruvate carboxylase f1077a mutant domain / Conserved carboxylase domain / Pyruvate carboxylase / Carboxylase, conserved domain / Conserved carboxylase domain / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase domain. / 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. / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / ATP-grasp fold, A domain / Biotin-requiring enzyme / Rudiment single hybrid motif / Cyclin A; domain 1 / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / ATP-grasp fold, B domain / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Aldolase class I / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Carbamoyl-phosphate synthase subdomain signature 2. / Arc Repressor Mutant, subunit A / Aldolase-type TIM barrel / TIM Barrel / Roll / Alpha-Beta Barrel / Beta Barrel / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-BTI / : / Pyruvate carboxylase / Pyruvate carboxylase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.71 Å
AuthorsTong, L. / Yu, L.P.C.
CitationJournal: Structure / Year: 2009
Title: A Symmetrical Tetramer for S. aureus Pyruvate Carboxylase in Complex with Coenzyme A.
Authors: Yu, L.P. / Xiang, S. / Lasso, G. / Gil, D. / Valle, M. / Tong, L.
History
DepositionMay 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_conn_type / 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_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_type.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: Pyruvate carboxylase
B: Pyruvate carboxylase
C: Pyruvate carboxylase
D: Pyruvate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)516,27013
Polymers514,7104
Non-polymers1,5609
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24520 Å2
ΔGint-79 kcal/mol
Surface area162590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.532, 257.154, 130.318
Angle α, β, γ (deg.)90.000, 114.350, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Pyruvate carboxylase


Mass: 128677.383 Da / Num. of mol.: 4 / Mutation: T908A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Gene: pycA, Pyruvate Carboxylase, SAV1114 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star(DE3) / References: UniProt: Q99UY8, UniProt: A0A0H3JRU9*PLUS
#2: Chemical
ChemComp-BTI / 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL


Mass: 228.311 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N2O2S
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


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

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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: 2.86 Å3/Da / Density % sol: 57.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 3350, 0.2M ammonium tartrate, pH 7.5, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.981 Å
DetectorType: r / Detector: CCD / Date: Apr 19, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.981 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 135160 / % possible obs: 86.6 % / Redundancy: 3 % / Rmerge(I) obs: 0.087 / Χ2: 1.054 / Net I/σ(I): 10.833
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.7-2.83.10.437120581.16677.5
2.8-2.913.20.356121241.14177.7
2.91-3.043.10.265122681.09878.9
3.04-3.23.10.191125311.08580.3
3.2-3.430.148129941.08183.5
3.4-3.662.90.111135991.07287.4
3.66-4.032.80.088142801.03291.3
4.03-4.612.80.073147390.96894.4
4.61-5.830.068152041.03797.2
5.8-303.30.058153630.92297.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 30.3 / Cor.coef. Fo:Fc: 61.29
Highest resolutionLowest resolution
Rotation3.5 Å10 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
COMO1.2phasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.71→29.95 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.882 / Occupancy max: 1 / Occupancy min: 1 / SU B: 32.142 / SU ML: 0.306 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.418 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.279 6799 5 %RANDOM
Rwork0.228 ---
obs0.23 135012 86.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 296.06 Å2 / Biso mean: 70.362 Å2 / Biso min: 22.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å21.36 Å2
2---1.21 Å20 Å2
3---1.66 Å2
Refinement stepCycle: LAST / Resolution: 2.71→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34236 0 91 0 34327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02234985
X-RAY DIFFRACTIONr_angle_refined_deg1.0871.96847339
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.19554329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.73924.8731660
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.147156202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.61915196
X-RAY DIFFRACTIONr_chiral_restr0.0740.25296
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0226435
X-RAY DIFFRACTIONr_nbd_refined0.2010.216596
X-RAY DIFFRACTIONr_nbtor_refined0.3050.224042
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.21026
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.26
X-RAY DIFFRACTIONr_mcbond_it0.2911.522153
X-RAY DIFFRACTIONr_mcangle_it0.522234923
X-RAY DIFFRACTIONr_scbond_it0.687314312
X-RAY DIFFRACTIONr_scangle_it1.1454.512416
LS refinement shellResolution: 2.71→2.777 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 405 -
Rwork0.326 7994 -
all-8399 -
obs--72.83 %
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)
12.0375-0.89031.1526.21290.33164.47150.1861-0.1045-0.403-0.2590.03441.41940.9914-0.5212-0.2205-0.1829-0.1549-0.0719-0.2514-0.0330.046720.904353.36020.4788
24.11291.2601-1.00352.77761.58335.37180.053-0.23330.3413-0.62390.12890.7293-0.2814-0.6178-0.18190.3991-0.2302-0.18160.02780.22390.15145.6941-51.862440.783
33.01530.9073-0.31794.33441.94113.8276-0.0921-0.0259-0.1258-0.1438-0.0411-0.5430.51620.24250.1332-0.0498-0.04530.2422-0.3346-0.0487-0.142747.934541.1023-16.8922
41.7567-0.10050.28845.1741.36184.8123-0.0154-0.162-0.30090.2967-0.0448-0.5840.67790.5280.06020.13630.0985-0.1787-0.03550.2319-0.092233.8574-48.686759.6504
51.5210.13920.18051.7109-0.0640.911-0.0090.0210.1854-0.04260.050.1743-0.1837-0.0998-0.041-0.5236-0.0205-0.0783-0.35770.062-0.340814.6735-10.1099-20.4767
60.97540.275-0.25872.7940.93962.04470.0546-0.09120.12180.1440.06340.344-0.188-0.424-0.118-0.1380.2360.03540.02170.0009-0.385315.38769.718662.1154
71.38080.55850.35871.34280.05232.9596-0.1728-0.0488-0.08950.02110.2094-0.3707-0.01370.4181-0.03660.0180.0697-0.0281-0.1697-0.1496-0.256550.248628.270947.4772
81.5079-0.4748-0.18691.1407-0.29291.1689-0.04060.00840.10010.18290.0405-0.2353-0.04330.04420.0002-0.5551-0.0023-0.0331-0.4453-0.0267-0.283343.8264-35.6309-5.1962
94.7115-2.88382.607419.7347-5.885717.9065-0.18790.46790.1409-0.03430.55080.9455-0.3024-1.0231-0.36290.11130.0502-0.0310.21660.03960.02411.002216.90128.4445
104.4995-0.44250.62634.4261-1.88433.8114-0.3005-0.23380.26880.39220.25530.44750.025-0.39010.0452-0.04470.03530.02750.0018-0.08720.01597.6102-15.941413.0008
1132.6353-9.3334-2.535826.029210.805411.7274-0.05710.223-0.69130.78560.1051-0.82570.67850.5802-0.0480.1053-0.0040.0880.2902-0.04580.174270.31162.164437.5416
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 167
2X-RAY DIFFRACTION1A239 - 494
3X-RAY DIFFRACTION2B36 - 167
4X-RAY DIFFRACTION2B239 - 494
5X-RAY DIFFRACTION3C36 - 167
6X-RAY DIFFRACTION3C239 - 494
7X-RAY DIFFRACTION4D36 - 167
8X-RAY DIFFRACTION4D239 - 494
9X-RAY DIFFRACTION5A495 - 1093
10X-RAY DIFFRACTION6B495 - 1093
11X-RAY DIFFRACTION7C495 - 1093
12X-RAY DIFFRACTION8D495 - 1093
13X-RAY DIFFRACTION9A1094 - 1178
14X-RAY DIFFRACTION10B1094 - 1178
15X-RAY DIFFRACTION11D1101 - 1178

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