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- PDB-2raa: Crystal structure of pyruvate oxidoreductase subunit PORC (EC 1.2... -

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Basic information

Entry
Database: PDB / ID: 2raa
TitleCrystal structure of pyruvate oxidoreductase subunit PORC (EC 1.2.7.1) (TM0015) from Thermotoga maritima at 2.12 A resolution
ComponentsPyruvate synthase subunit porC
KeywordsOXIDOREDUCTASE / TM0015 / Pyruvate oxidoreductase subunit PORC (EC 1.2.7.1) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


pyruvate synthase / pyruvate synthase activity
Similarity search - Function
2-oxoacid:acceptor oxidoreductase, gamma subunit, pyruvate/2-ketoisovalerate / : / : / Pyruvate-ferredoxin Oxidoreductase; domain 3 / Pyruvate-ferredoxin oxidoreductase, PFOR, domain III / Pyruvate-flavodoxin oxidoreductase, central domain / Pyruvate/ketoisovalerate oxidoreductase, catalytic domain / Pyruvate ferredoxin/flavodoxin oxidoreductase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Pyruvate synthase subunit PorC
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.12 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of pyruvate oxidoreductase subunit PORC (EC 1.2.7.1) (TM0015) from Thermotoga maritima at 2.12 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyruvate synthase subunit porC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2353
Polymers23,0431
Non-polymers1922
Water48627
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.252, 57.252, 147.151
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Pyruvate synthase subunit porC / Pyruvate oxidoreductase gamma chain / POR / Pyruvic-ferredoxin oxidoreductase subunit gamma


Mass: 23042.654 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Species: Thermotoga maritima / Strain: MSB8, DSM 3109, JCM 10099 / Gene: TM0015, porC, porG / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: O05650, pyruvate synthase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
12.6252.99TWO CRYSTALS WERE USED FOR THE SOLUTION OF THIS STRUCTURE. A 2.35 ANGSTROM MAD DATA COLLECTED FROM ONE CRYSTAL WAS USED TO PHASE AND TRACE AN INITIAL MODEL. THE MODEL WAS THEN REFINED USING THE AMPLITUDES FROM A SECOND CRYSTAL THAT DIFFRACTED TO 2.12 ANGSTROM.
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, sitting drop4NANODROP, 0.8M Ammonium sulfate, 0.1M Citrate pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
2932vapor diffusion, sitting drop3.93NANODROP, 0.86M Ammonium sulfate, 0.1M Citrate pH 3.93, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.211
SYNCHROTRONSSRL BL11-120.91837, 0.97925, 0.97895
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDAug 30, 2007
MARMOSAIC 325 mm CCD2CCDJun 3, 2007Flat mirror (vertical focusing)
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1KOHZU: Double crystal Si(111)SINGLE WAVELENGTHMx-ray1
2Single crystal Si(111) bent (horizontal focusing)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.918371
30.979251
40.978951
ReflectionResolution: 2.12→45.175 Å / Num. obs: 14544 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 56.283 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 16.76
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.12-2.20.612.3515514801,299.7
2.2-2.280.4853439512771,299.3
2.28-2.390.3564525815271,299.8
2.39-2.510.2755.1468913641,2100
2.51-2.670.2037.1496714481,299.4
2.67-2.880.39511788314841,299.6
2.88-3.160.28516.9969013931,299.1
3.16-3.620.10427.91014414821,299.1
3.62-4.550.04439.5990914871,298.8
4.55-45.1750.02945.8976916021,296.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.12→45.175 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 15.077 / SU ML: 0.172 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.193 / ESU R Free: 0.173
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. SO4 IONS FROM THE CRYSTALLIZATION SOLUTION ARE MODELED. 5. THE FOLLOWING LOOPS HAVE POOR OR NO DENSITY: 5-7, 43-50, 62-69, 165-169. THUS, THE MODEL IN THESE REGIONS IS NOT RELIABLE. N-TERMINUS AS WELL AS PURIFICATION TAG ARE DISORDERED. 6. A FEW NON-WATER DENSITY BLOBS OUTSIDE THE PROTEIN ARE LEFT UNINTERPRETED.
RfactorNum. reflection% reflectionSelection details
Rfree0.251 699 4.8 %RANDOM
Rwork0.215 ---
obs0.217 14517 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 49.003 Å2
Baniso -1Baniso -2Baniso -3
1-1.79 Å20 Å20 Å2
2--1.79 Å20 Å2
3----3.58 Å2
Refinement stepCycle: LAST / Resolution: 2.12→45.175 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1349 0 10 27 1386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221402
X-RAY DIFFRACTIONr_bond_other_d0.0020.02955
X-RAY DIFFRACTIONr_angle_refined_deg1.691.9761898
X-RAY DIFFRACTIONr_angle_other_deg0.97132322
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0935180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02623.8163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.3615236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4751512
X-RAY DIFFRACTIONr_chiral_restr0.1050.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021563
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02284
X-RAY DIFFRACTIONr_nbd_refined0.2290.2298
X-RAY DIFFRACTIONr_nbd_other0.2030.2972
X-RAY DIFFRACTIONr_nbtor_refined0.1860.2675
X-RAY DIFFRACTIONr_nbtor_other0.0950.2773
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.236
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1350.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.220.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.24
X-RAY DIFFRACTIONr_mcbond_it2.4093929
X-RAY DIFFRACTIONr_mcbond_other0.5153365
X-RAY DIFFRACTIONr_mcangle_it3.53751422
X-RAY DIFFRACTIONr_scbond_it5.9658547
X-RAY DIFFRACTIONr_scangle_it8.74811473
LS refinement shellResolution: 2.12→2.175 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 57 -
Rwork0.312 964 -
all-1021 -
obs--99.71 %
Refinement TLS params.Method: refined / Origin x: 12.2125 Å / Origin y: 18.0783 Å / Origin z: 57.1044 Å
111213212223313233
T-0.2013 Å20.0181 Å20.025 Å2-0.0018 Å2-0.0178 Å2---0.0102 Å2
L1.9677 °21.1244 °21.965 °2-2.2797 °21.9853 °2--4.4504 °2
S0.0767 Å °0.3603 Å °-0.1098 Å °0.0063 Å °0.176 Å °0.0019 Å °-0.1645 Å °0.1088 Å °-0.2527 Å °

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