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- PDB-3bg5: Crystal Structure of Staphylococcus Aureus Pyruvate Carboxylase -

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Basic information

Entry
Database: PDB / ID: 3bg5
TitleCrystal Structure of Staphylococcus Aureus Pyruvate Carboxylase
ComponentsPyruvate carboxylase
KeywordsLIGASE / TIM barrel / ATP-binding / Nucleotide-binding / 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
Helix Hairpins - #310 / 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 ...Helix Hairpins - #310 / 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 / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Rudiment single hybrid motif / Single hybrid motif / ATP-grasp fold, A domain / Cyclin A; domain 1 / ATP-grasp fold, B domain / Pre-ATP-grasp domain superfamily / Helix Hairpins / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Helix non-globular / Special / Aldolase class I / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Carbamoyl-phosphate synthase subdomain signature 2. / Aldolase-type TIM barrel / Arc Repressor Mutant, subunit A / 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'-TRIPHOSPHATE / Chem-BTI / : / PYRUVIC ACID / Pyruvate carboxylase / Pyruvate carboxylase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsXiang, S. / Tong, L.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Crystal structures of human and Staphylococcus aureus pyruvate carboxylase and molecular insights into the carboxyltransfer reaction.
Authors: Xiang, S. / Tong, L.
History
DepositionNov 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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)527,17218
Polymers524,6734
Non-polymers2,50014
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24020 Å2
MethodPISA
2
A: Pyruvate carboxylase
C: Pyruvate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)264,09310
Polymers262,3362
Non-polymers1,7578
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7850 Å2
MethodPISA
3
B: Pyruvate carboxylase
D: Pyruvate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)263,0798
Polymers262,3362
Non-polymers7436
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.428, 256.083, 126.010
Angle α, β, γ (deg.)90.00, 109.47, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22D
32B
13A
23B
33C
43D
53A
63B
73C
83D

NCS domain segments:

Refine code: 6

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPASNASNAA495 - 1093487 - 1084
211ASPASPASNASNBB495 - 1093487 - 1084
311ASPASPASNASNCC495 - 1093487 - 1084
411ASPASPASNASNDD495 - 1093487 - 1084
112LYSLYSGLUGLUAA1101 - 11781092 - 1169
212LYSLYSGLUGLUDD1101 - 11781092 - 1169
312LYSLYSGLUGLUBB1101 - 11781092 - 1169
113GLNGLNILEILEAA36 - 16726 - 157
213GLNGLNILEILEBB36 - 16726 - 157
313GLNGLNILEILECC36 - 16726 - 157
413GLNGLNILEILEDD36 - 16726 - 157
523VALVALLEULEUAA267 - 494257 - 486
623VALVALLEULEUBB267 - 494257 - 486
723VALVALLEULEUCC267 - 494257 - 486
823VALVALLEULEUDD267 - 494257 - 486

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Pyruvate carboxylase /


Mass: 131168.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: pycA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Star / References: UniProt: Q99UY8, UniProt: A0A0H3JRU9*PLUS
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: 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
#4: Chemical
ChemComp-PYR / PYRUVIC ACID / Pyruvic acid


Mass: 88.062 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H4O3
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, 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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 200 mM ammonium tartrate, 20% (w/v) PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 27, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 145707 / Num. obs: 131856 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 16.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.416 / % possible all: 97.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0003refinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.89 / SU B: 33.842 / SU ML: 0.305 / Cross valid method: THROUGHOUT / ESU R Free: 0.392 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2676 6975 5 %RANDOM
Rwork0.21458 ---
obs0.21724 131856 98.48 %-
all-138831 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.705 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20 Å21.92 Å2
2---2.52 Å20 Å2
3---2.79 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34293 0 150 0 34443
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02235097
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1061.95647498
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.28854336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.64824.8741662
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.792156214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.35815196
X-RAY DIFFRACTIONr_chiral_restr0.0760.25309
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0226521
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.216089
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.224042
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2980
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.381.522162
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.69234981
X-RAY DIFFRACTIONr_scbond_it0.786314398
X-RAY DIFFRACTIONr_scangle_it1.3494.512517
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A4764loose positional0.725
12B4764loose positional0.875
13C4764loose positional1.525
14D4764loose positional0.585
21A576loose positional0.745
22D576loose positional1.155
23B576loose positional0.725
31A2842loose positional0.65
32B2842loose positional0.815
33C2842loose positional0.615
34D2842loose positional0.725
11A4764loose thermal3.1510
12B4764loose thermal3.8510
13C4764loose thermal3.8910
14D4764loose thermal5.5310
21A576loose thermal1.9410
22D576loose thermal4.3110
23B576loose thermal5.4810
31A2842loose thermal4.4610
32B2842loose thermal4.4510
33C2842loose thermal2.5210
34D2842loose thermal2.2610
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.446 496 -
Rwork0.34 9448 -
obs--96.51 %
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)
11.0745-0.8439-0.54834.239-0.42571.96960.0844-0.14420.1275-0.25970.0296-0.8931-0.22220.0853-0.114-0.1559-0.04190.0355-0.2006-0.02870.075575.554251.84550.3552
21.23750.65960.15283.2343-1.07461.8605-0.04640.0346-0.0106-0.27140.00140.225-0.273-0.0550.0449-0.0404-0.0182-0.2282-0.22610.0159-0.112848.384964.0447-17.0086
31.2846-0.031-0.27413.20830.10863.04170.1023-0.25910.22160.3607-0.01740.3635-0.2882-0.2333-0.0849-0.06190.03930.197-0.091-0.1301-0.104863.002153.724259.6705
42.71160.92190.18572.2056-0.26054.63570.1676-0.1521-0.0663-0.4880.1448-0.72260.16090.4158-0.3124-0.0018-0.23240.1634-0.0962-0.17170.05291.3217156.694740.7595
50.53850.1808-0.02620.97920.13530.4887-0.02010.0976-0.0959-0.1850.0396-0.20550.13420.048-0.0195-0.1329-0.02010.1126-0.0334-0.02820.031181.8613115.2077-20.5261
60.48620.03030.23661.3894-0.52421.03770.0087-0.12470.00820.12940.028-0.12590.00910.2772-0.0367-0.02070.1866-0.07390.16080.0087-0.167381.363495.21162.1295
71.08640.2856-0.4520.60520.09581.6758-0.1343-0.05090.00320.02640.16860.21580.0676-0.2164-0.03430.02890.09630.014-0.02760.0824-0.048546.390976.747747.4175
80.6082-0.35150.08160.62620.21410.3144-0.03450.0025-0.01990.03270.03750.1115-0.02640.0127-0.003-0.1202-0.0136-0.0002-0.06450.05170.047752.8383140.6425-5.123
92.202-0.12161.06092.62742.74938.7515-0.36530.4488-0.0479-0.0180.3944-0.22760.1990.6581-0.0291-0.00160.05650.0354-0.0059-0.0604-0.001885.617888.086928.2467
1025.1843-9.94943.005516.276-7.22227.85140.04760.28540.46260.28990.450.7238-0.5344-0.5315-0.4976-0.01190.087-0.0063-0.01030.0085-0.004826.4392102.979237.5781
114.5213-2.694-0.37565.11171.72373.2862-0.4154-0.3297-0.17980.4640.3876-0.23030.22120.22540.0279-0.2790.008-0.0703-0.15330.0352-0.141889.1366120.831612.9802
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA36 - 16726 - 157
2X-RAY DIFFRACTION1AA239 - 494229 - 486
3X-RAY DIFFRACTION2CC36 - 16726 - 157
4X-RAY DIFFRACTION2CC239 - 494229 - 486
5X-RAY DIFFRACTION3DD36 - 16726 - 157
6X-RAY DIFFRACTION3DD239 - 494229 - 486
7X-RAY DIFFRACTION4BB36 - 16726 - 157
8X-RAY DIFFRACTION4BB239 - 494229 - 486
9X-RAY DIFFRACTION5AA495 - 1093487 - 1084
10X-RAY DIFFRACTION6BB495 - 1093487 - 1084
11X-RAY DIFFRACTION7CC495 - 1093487 - 1084
12X-RAY DIFFRACTION8DD495 - 1093487 - 1084
13X-RAY DIFFRACTION9AA1094 - 11781085 - 1169
14X-RAY DIFFRACTION10DD1101 - 11781092 - 1169
15X-RAY DIFFRACTION11BB1094 - 11781085 - 1169

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