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- PDB-1w62: proline racemase in complex with one molecule of pyrrole-2-carbox... -

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Basic information

Entry
Database: PDB / ID: 1w62
Titleproline racemase in complex with one molecule of pyrrole-2-carboxylic acid (hemi form)
ComponentsProline racemase A
KeywordsRACEMASE / RACEMASE PYRIDOXAL PHOSPHATE-INDEPENDENT / STEREO INVERSION / B-CELL MITOGEN / HOMODIMER / ALPHA/BETA DOMAINS
Function / homology
Function and homology information


proline racemase activity / proline racemase / 4-hydroxyproline epimerase activity / extracellular region / membrane / cytoplasm
Similarity search - Function
Proline racemase family / Proline racemase / Diaminopimelate Epimerase; Chain A, domain 1 / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha Beta
Similarity search - Domain/homology
PYRROLE-2-CARBOXYLATE / Proline racemase A
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBuschiazzo, A. / Alzari, P.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2006
Title: Crystal structure, catalytic mechanism, and mitogenic properties of Trypanosoma cruzi proline racemase.
Authors: Buschiazzo, A. / Goytia, M. / Schaeffer, F. / Degrave, W. / Shepard, W. / Gregoire, C. / Chamond, N. / Cosson, A. / Berneman, A. / Coatnoan, N. / Alzari, P.M. / Minoprio, P.
History
DepositionAug 12, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 13, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity.pdbx_description / _entity_name_com.name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_seq_type
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proline racemase A
B: Proline racemase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,7033
Polymers91,5922
Non-polymers1101
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)136.018, 89.382, 84.456
Angle α, β, γ (deg.)90.00, 125.98, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.4914, -0.2728, 0.8271), (-0.3078, -0.834, -0.4579), (0.8147, -0.4796, 0.3259)23.6617, 14.411, -9.4706
2given(-0.22536, -0.3246, 0.91861), (-0.28745, -0.87874, -0.38103), (0.93091, -0.34992, 0.10472)13.266, 14.232, -10.04

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Components

#1: Protein Proline racemase A / TcPA45-A / TcPRACA / rTcPA45 / B-CELL MITOGEN


Mass: 45796.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Gene: PA45-A, Tc00.1047053506795.80 / Plasmid: PET28B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4DA80, proline racemase
#2: Chemical ChemComp-PYC / PYRROLE-2-CARBOXYLATE


Mass: 110.091 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST 31 AA IN Q9NCP4 CONSTITUTE A SIGNAL-PEPTIDE AND WERE EXCLUDED IN THE CONSTRUCTION USED ...THE FIRST 31 AA IN Q9NCP4 CONSTITUTE A SIGNAL-PEPTIDE AND WERE EXCLUDED IN THE CONSTRUCTION USED FOR CRYSTALLIZATION. THE LAST 21 AA IN THE CRYSTALLIZED PROTEIN DERIVE FROM THE EXPRESSION PLASMID (CONTAIN THE 6XHIS-TAG)

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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: 2.6 Å3/Da / Density % sol: 53.5 %
Crystal growpH: 5.6
Details: 15% PEG 4000,100MM NH4ACETATE 50MM NA3CITRATE.H2O,PH5.6, pH 5.60

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Details: SAGITALLY FOCUSING GE(220) AND A MULTILAYER
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.5→60 Å / Num. obs: 27664 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Biso Wilson estimate: 54.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 4 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W61

1w61


Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.921 / SU B: 16.435 / SU ML: 0.187 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.645 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2778 10 %RANDOM
Rwork0.17 ---
obs0.177 24875 97.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å2-0.66 Å2
2---0.38 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5395 0 8 151 5554
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0225512
X-RAY DIFFRACTIONr_bond_other_d0.0010.025048
X-RAY DIFFRACTIONr_angle_refined_deg1.7661.957483
X-RAY DIFFRACTIONr_angle_other_deg0.88311748
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1145711
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.37124.641237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.16515893
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4591529
X-RAY DIFFRACTIONr_chiral_restr0.0990.2850
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026217
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021072
X-RAY DIFFRACTIONr_nbd_refined0.2080.21055
X-RAY DIFFRACTIONr_nbd_other0.1850.25132
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22699
X-RAY DIFFRACTIONr_nbtor_other0.0890.23443
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2198
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2170.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2870.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0111.54471
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.20125710
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.87532219
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9674.51773
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.298 174
Rwork0.229 1863
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)
10.6896-0.5563-0.29381.48390.231.1869-0.06750.09710.02390.08330.0170.01070.24270.01750.0505-0.1003-0.01570.02880.0164-0.0057-0.071528.476-16.19520.299
21.68120.0977-0.3481.89480.92411.4313-0.09820.4895-0.0273-0.28880.01530.1483-0.0535-0.15250.0829-0.086-0.02480.01430.151-0.0101-0.179123.647-18.436-2.319
30.75130.1349-0.05220.93410.67620.9118-0.03830.05270.1069-0.0598-0.0632-0.0451-0.0303-0.12640.1015-0.1090.02290.01160.0550.02210.007331.29310.29628.175
40.80370.220.08972.1360.17062.18360.05860.08220.0801-0.17260.02520.0334-0.1642-0.1395-0.0838-0.16590.08450.0410.00130.0355-0.023711.06123.54918.469
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A44 - 186
2X-RAY DIFFRACTION1A369 - 393
3X-RAY DIFFRACTION2A190 - 367
4X-RAY DIFFRACTION3B44 - 186
5X-RAY DIFFRACTION3B369 - 393
6X-RAY DIFFRACTION4B190 - 367

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