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- PDB-3hb9: Crystal Structure of S. aureus Pyruvate Carboxylase A610T Mutant -

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Basic information

Entry
Database: PDB / ID: 3hb9
TitleCrystal Structure of S. aureus Pyruvate Carboxylase A610T 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 / cytoplasm
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. / 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 / Biotin-requiring enzyme / ATP-grasp fold, A domain / Rudiment single hybrid motif / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Cyclin A; domain 1 / 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 / Carbamoyl-phosphate synthase subdomain signature 2. / Arc Repressor Mutant, subunit A / Aldolase-type TIM barrel / TIM Barrel / Roll / Alpha-Beta Barrel / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / 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: 2.9 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)516,93714
Polymers514,9504
Non-polymers1,98710
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24210 Å2
ΔGint-73 kcal/mol
Surface area158620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.566, 256.763, 126.485
Angle α, β, γ (deg.)90.000, 109.650, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Pyruvate carboxylase


Mass: 128737.430 Da / Num. of mol.: 4 / Mutation: A610T
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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn

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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: 2.87 Å3/Da / Density % sol: 57.11 %
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: X4A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 19, 2008 / Details: On Huber Eulerian cradle
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 124542 / % possible obs: 92.5 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.075 / Χ2: 0.981 / Net I/σ(I): 12.217
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.9-32.50.422112391.1284
3-3.122.50.318113761.11784.5
3.12-3.272.50.214116221.0886.5
3.27-3.442.50.16119461.07489
3.44-3.652.50.112123631.04391.7
3.65-3.932.50.082127470.99795
3.93-4.332.60.063130870.9597.3
4.33-4.952.70.052132770.91198.6
4.95-6.232.80.053134120.91599.4
6.23-302.90.045134730.75499

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 35.5 / Cor.coef. Fo:Fc: 51.6
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: 2.9→30 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.868 / Occupancy max: 1 / Occupancy min: 1 / SU B: 39.051 / SU ML: 0.344 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.441 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.266 5983 5 %RANDOM
Rwork0.22 ---
obs0.222 118525 92.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 211.92 Å2 / Biso mean: 62.163 Å2 / Biso min: 16.69 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å20 Å20.96 Å2
2--1.22 Å20 Å2
3---0.59 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33726 0 118 0 33844
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02234492
X-RAY DIFFRACTIONr_angle_refined_deg0.9561.96946671
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.53154257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.4624.8231640
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.915156116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.67715196
X-RAY DIFFRACTIONr_chiral_restr0.0640.25215
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0226053
X-RAY DIFFRACTIONr_nbd_refined0.1830.216294
X-RAY DIFFRACTIONr_nbtor_refined0.3010.223812
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.2911
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1090.26
X-RAY DIFFRACTIONr_mcbond_it0.2061.521771
X-RAY DIFFRACTIONr_mcangle_it0.375234348
X-RAY DIFFRACTIONr_scbond_it0.415314177
X-RAY DIFFRACTIONr_scangle_it0.7274.512323
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 402 -
Rwork0.305 7456 -
all-7858 -
obs--83.9 %
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)
12.0649-0.8812-1.01166.6531-0.37084.81850.0984-0.02920.3318-0.35360.0057-1.4697-0.93470.43-0.1041-0.2049-0.11850.0598-0.38130.0025-0.013775.266451.65030.668
22.61290.80150.36885.386-2.68964.8786-0.2235-0.08380.14980.1553-0.09020.4267-0.6909-0.34240.3138-0.0702-0.0104-0.3151-0.3534-0.0536-0.105148.61164.2735-16.7876
32.3563-0.2555-0.98976.4495-4.18818.90740.0695-0.03080.34840.3379-0.09640.3097-1.0801-0.62580.02690.19990.07250.1693-0.1254-0.1954-0.033562.8075153.618559.9226
43.84260.6971.89812.7045-1.86057.00250.0277-0.66680.0422-0.29190.0932-0.50420.3628-0.0331-0.12080.1855-0.28990.06560.2162-0.23510.155590.7053157.361540.625
51.27990.2271-0.05881.4836-0.12470.8629-0.01580.0866-0.1962-0.06110.0248-0.18630.17140.0967-0.0091-0.5027-0.00260.0561-0.403-0.0798-0.389782.191115.0155-20.2786
60.96020.16610.20781.8692-0.46061.70770.0527-0.1315-0.02490.03810.0784-0.2535-0.03220.3259-0.1311-0.37260.0964-0.0243-0.1309-0.0387-0.408780.950695.276862.5666
72.03690.3727-0.30680.89610.1092.6376-0.0922-0.17160.0751-0.05250.03080.2959-0.0107-0.42620.0614-0.31360.0015-0.049-0.29830.0422-0.296945.899577.341348.0729
81.5578-0.46770.17240.9080.09331.1627-0.0092-0.0052-0.0940.11280.03710.19720.0297-0.0272-0.028-0.5119-0.00950.0383-0.5540.0327-0.361753.0378140.5672-5.2422
95.27440.13670.59355.0422.50536.3682-0.16040.0883-0.0718-0.33170.3232-0.5114-0.10450.6495-0.1627-0.11320.04690.0606-0.0105-0.0209-0.122485.535687.551728.8671
108.0142-0.4377-1.0248.67891.52833.9996-0.1863-0.3957-0.12380.25550.1722-0.12250.17890.34980.0141-0.27630.0146-0.0708-0.14010.0776-0.349689.3993121.068213.2063
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 167
2X-RAY DIFFRACTION1A239 - 494
3X-RAY DIFFRACTION2C36 - 167
4X-RAY DIFFRACTION2C239 - 494
5X-RAY DIFFRACTION3D36 - 167
6X-RAY DIFFRACTION3D239 - 494
7X-RAY DIFFRACTION4B36 - 167
8X-RAY DIFFRACTION4B239 - 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

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