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- PDB-1rqh: Propionibacterium shermanii transcarboxylase 5S subunit bound to ... -

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Basic information

Entry
Database: PDB / ID: 1rqh
TitlePropionibacterium shermanii transcarboxylase 5S subunit bound to pyruvic acid
Componentstranscarboxylase 5S subunit
KeywordsTRANSFERASE / TIM-barrel / carbamylated lysine / transcarboxylase / cobalt / pyruvic acid
Function / homology
Function and homology information


methylmalonyl-CoA carboxytransferase / methylmalonyl-CoA carboxytransferase activity / pyruvate carboxylase activity / gluconeogenesis / metal ion binding / cytoplasm
Similarity search - Function
: / Carboxylase, conserved domain / Conserved carboxylase domain / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase domain. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / PYRUVIC ACID / : / Methylmalonyl-CoA carboxyltransferase 5S subunit
Similarity search - Component
Biological speciesPropionibacterium freudenreichii subsp. shermanii (bacteria)
MethodX-RAY DIFFRACTION / Isomorphous replacement / Resolution: 2 Å
AuthorsHall, P.R. / Zheng, R. / Antony, L. / Pusztai-Carey, M. / Carey, P.R. / Yee, V.C.
Citation
Journal: Embo J. / Year: 2004
Title: Transcarboxylase 5S structures: assembly and catalytic mechanism of a multienzyme complex subunit.
Authors: Hall, P.R. / Zheng, R. / Antony, L. / Pusztai-Carey, M. / Carey, P.R. / Yee, V.C.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2004
Title: Expression and crystallization of several forms of the Propionibacterium shermanii transcarboxylase 5S subunit.
Authors: Hall, P.R. / Zheng, R. / Pusztai-Carey, M. / van den Akker, F. / Carey, P.R. / Yee, V.C.
History
DepositionDec 5, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 23, 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_alt_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_alt_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.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2
Remark 999SEQUENCE RESIDUE 184 EXISTS IN TWO ALTERNATE CONFORMATIONS: KCX, CARBAMYLATED LYSINE, AND LYS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: transcarboxylase 5S subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7993
Polymers59,6521
Non-polymers1472
Water7,476415
1
A: transcarboxylase 5S subunit
hetero molecules

A: transcarboxylase 5S subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,5996
Polymers119,3052
Non-polymers2944
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_754-x+2,y,-z-1/21
Unit cell
Length a, b, c (Å)96.025, 145.720, 78.747
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-607-

HOH

21A-676-

HOH

31A-1000-

HOH

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Components

#1: Protein transcarboxylase 5S subunit


Mass: 59652.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: RESIDUE 184 EXISTS IN TWO ALTERNATE CONFORMATIONS: KCX AND LYS
Source: (gene. exp.) Propionibacterium freudenreichii subsp. shermanii (bacteria)
Species: Propionibacterium freudenreichii / Strain: subsp. shermanii / Gene: 5S / Plasmid: pETBlue-2 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner(DE3)pLacI
References: GenBank: 38304072, UniProt: Q70AC7*PLUS, methylmalonyl-CoA carboxytransferase
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.31 Å3/Da / Density % sol: 46.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG 4000, Tris, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 22, 2003
RadiationMonochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 37671 / Num. obs: 34906 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 16.3
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 4.3 / % possible all: 80.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: Isomorphous replacement
Starting model: PDB ENTRY 1RQB

1rqb


Resolution: 2→28.09 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 370661.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: RESIDUE 184 EXISTS IN TWO ALTERNATE CONFORMATIONS: KCX AND LYS.
RfactorNum. reflection% reflectionSelection details
Rfree0.197 1657 4.7 %RANDOM
Rwork0.164 ---
all0.166 37671 --
obs0.166 34906 92.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.0483 Å2 / ksol: 0.32071 e/Å3
Displacement parametersBiso mean: 32.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2--0.13 Å20 Å2
3----0.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2→28.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3676 0 7 415 4098
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_mcbond_it1.933
X-RAY DIFFRACTIONc_mcangle_it2.583.5
X-RAY DIFFRACTIONc_scbond_it3.283.5
X-RAY DIFFRACTIONc_scangle_it4.424
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.244 260 5.1 %
Rwork0.206 4845 -
obs-5105 82.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP2.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMLIG_DUNDEE.TOP
X-RAY DIFFRACTION3WATER_REP.PARAM
X-RAY DIFFRACTION4LIG_DUNDEE.PAR

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