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- PDB-1w61: proline racemase in complex with 2 molecules of pyrrole-2-carboxy... -

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Basic information

Entry
Database: PDB / ID: 1w61
Titleproline racemase in complex with 2 molecules of pyrrole-2-carboxylic acid (holo form)
ComponentsB-CELL MITOGEN
KeywordsRACEMASE / RACEMASE PYRIDOXAL PHOSPHATE-INDEPENDENT / STEREO INVERSION / B-CELL MITOGEN / ACID/BASE CATALYSIS / HOMODIMER / ALPHA/BETA DOMAINS
Function / homology
Function and homology information


proline racemase activity / proline racemase / 4-hydroxyproline epimerase activity / multicellular organism development / 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 / Proline racemase A
Similarity search - Component
Biological speciesTRYPANOSOMA CRUZI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBuschiazzo, A. / Alzari, P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: Crystal Structure,Catalytic Mechanism and Mitogenic Properties of Trypanosoma Cruzi Proline Racemase
Authors: Buschiazzo, A. / Goytia, M. / Shaeffer, F. / Degrave, W. / Shepard, W. / Gregoire, C. / Chamond, N. / Cosson, A. / Berneman, A. / Coatnoan, N. / Alzari, P. / Minoprio, P.
History
DepositionAug 11, 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 1.2May 1, 2024Group: 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: B-CELL MITOGEN
B: B-CELL MITOGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,8134
Polymers91,5922
Non-polymers2202
Water6,449358
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)131.153, 91.209, 85.983
Angle α, β, γ (deg.)90.00, 126.52, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.4124, 0.2854, 0.8651), (0.3159, -0.8459, 0.4297), (0.8545, 0.4505, 0.2587)
Vector: 5.0503, 17.6479, -9.6554)

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Components

#1: Protein B-CELL MITOGEN / PROLINE RACEMASE


Mass: 45796.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA CRUZI (eukaryote) / Strain: CL BRENER / Plasmid: PET28B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9NCP4, UniProt: Q4DA80*PLUS, proline racemase
#2: Chemical ChemComp-PYC / PYRROLE-2-CARBOXYLATE


Mass: 110.091 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H4NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST 31 AA IN Q9NCP4 CONSTITUTE A SIGNAL PEPTIDE AND THEY WERE REMOVED IN THE CONSTRUCTION ...THE FIRST 31 AA IN Q9NCP4 CONSTITUTE A SIGNAL PEPTIDE AND THEY WERE REMOVED IN THE CONSTRUCTION USED FOR CRYSTALLIZATION. THE LAST 21 RESIDUES IN THE CRYSTALLIZED PROTEIN ARE CODED BY THE EXPRESSION PLASMID (INCLUDES 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: 2.5 Å3/Da / Density % sol: 50.8 %
Description: THE INITIAL MODEL WAS OBTAINED USING ANOMALOUS DIFFRACTION ON SE-MET SUBSTITUTED CRYSTALS. THE REFINEMENT OF THIS INITIAL MODEL WAS NOT COMPLETED -RES 3 ANGSTROMS- BUT USED SUCCESFULLY ...Description: THE INITIAL MODEL WAS OBTAINED USING ANOMALOUS DIFFRACTION ON SE-MET SUBSTITUTED CRYSTALS. THE REFINEMENT OF THIS INITIAL MODEL WAS NOT COMPLETED -RES 3 ANGSTROMS- BUT USED SUCCESFULLY AS MOLECULAR REPLACEMENT PROBE
Crystal growpH: 5.6
Details: 15% PEG 4000,100MM NH4ACETATE 50MM NA3CITRATE.2H2O,PH5.6, pH 5.60

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0072
DetectorType: ADSC CCD / Detector: CCD / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0072 Å / Relative weight: 1
ReflectionResolution: 2.1→69.2 Å / Num. obs: 46967 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 23.92 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.4
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 7.7 / % possible all: 94.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MODEL OF THE SAME PROTEIN OBTAINED BY SAD

Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.436 / SU ML: 0.093 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.193 2331 5.04 %RANDOM
Rwork0.148 ---
obs0.15 46958 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.425 Å20 Å20.727 Å2
2---0.744 Å20 Å2
3---0.183 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5374 0 16 358 5748
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0225501
X-RAY DIFFRACTIONr_bond_other_d0.0060.025025
X-RAY DIFFRACTIONr_angle_refined_deg1.721.9517472
X-RAY DIFFRACTIONr_angle_other_deg0.886311695
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.95708
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.85524.681235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.40615887
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.611528
X-RAY DIFFRACTIONr_chiral_restr0.1080.2849
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026202
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021069
X-RAY DIFFRACTIONr_nbd_refined0.1950.2955
X-RAY DIFFRACTIONr_nbd_other0.1980.24902
X-RAY DIFFRACTIONr_nbtor_refined0.1750.22682
X-RAY DIFFRACTIONr_nbtor_other0.0910.23090
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2345
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3460.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2890.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2270.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7781.54486
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.69625703
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.01432224
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2394.51769
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: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.227 152
Rwork0.141 2961
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)
10.49590.147-0.32491.3509-0.40660.7505-0.00560.0021-0.0362-0.2266-0.0123-0.01870.1498-0.03860.01780.0111-0.00310.0023-0.0448-0.0013-0.053712.8120.65313.812
20.6915-0.16050.16261.6905-0.67710.7799-0.0802-0.1286-0.01680.3087-0.0218-0.1823-0.12160.05590.10190.0147-0.0048-0.0408-0.0080.0368-0.070217.537-1.19636.481
30.54750.0540.07760.8366-0.33670.6733-0.0303-0.00550.024-0.10390.031-0.01370.0037-0.0201-0.00070.0066-0.00860.002-0.0309-0.0013-0.061211.76126.9845.293
40.80290.0454-0.17751.03980.2090.89750.051-0.09450.0955-0.02640.0435-0.1807-0.07740.1254-0.0944-0.0462-0.040.0421-0.0344-0.0349-0.007228.67740.10514.433
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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