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- PDB-4q2h: Crystal structure of probable proline racemase from agrobacterium... -

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Basic information

Entry
Database: PDB / ID: 4q2h
TitleCrystal structure of probable proline racemase from agrobacterium radiobacter K84, TARGET EFI-506561, with bound carbonate
ComponentsProline racemase protein
KeywordsISOMERASE / PROLINE RACEMASE FAMILY / PROBABLE PROLINE RACEMASE / ENZYME FUNCTION INITIATIVE / EFI / STRUCTURAL GENOMICS
Function / homology
Function and homology information


4-hydroxyproline epimerase / 4-hydroxyproline epimerase activity
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
BICARBONATE ION / 4-hydroxyproline 2-epimerase 1
Similarity search - Component
Biological speciesAgrobacterium radiobacter K84 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPatskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Glenn, A.S. ...Patskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Glenn, A.S. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal Structure of Proline Racemase Arad_0731 from Agrobacterium Radiobacter, Target Efi-506561
Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Glenn, A.S. / Chowdhury, S. / Evans, B. / Hammonds, J. ...Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Glenn, A.S. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionApr 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Sep 20, 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)79,0265
Polymers78,8122
Non-polymers2143
Water12,232679
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-20 kcal/mol
Surface area24360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.430, 129.470, 178.703
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-629-

HOH

21A-681-

HOH

31A-836-

HOH

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Components

#1: Protein Proline racemase protein


Mass: 39406.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium radiobacter K84 (bacteria)
Strain: K84 / ATCC BAA-868 / Gene: Arad_0731 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B9J8G8
#2: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 679 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 15 MM BIS-TRIS, 500 MM NACL, 10% GLYCEROL, 5 MM DTT, TEV PROTEASE (1:100 RATIO); RESERVOIR: 0.4 M POTASSIUM PHOSPHATE MONOBASIC, 16% PEG8000, 20% GLYCEROL, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 26, 2014 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 72154 / % possible obs: 99.9 % / Observed criterion σ(I): -5 / Redundancy: 7.3 % / Biso Wilson estimate: 25.997 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 20.9
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.91 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.8.0069refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4LB0

4lb0


Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / SU B: 4.624 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1757 2156 3 %RANDOM
Rwork0.14656 ---
obs0.14744 69949 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.503 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å2-0 Å2-0 Å2
2--1.83 Å20 Å2
3----1.36 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5102 0 14 679 5795
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195312
X-RAY DIFFRACTIONr_bond_other_d0.0010.025172
X-RAY DIFFRACTIONr_angle_refined_deg1.3491.9767248
X-RAY DIFFRACTIONr_angle_other_deg0.74311906
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9685712
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.79723.462208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.11515854
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2071543
X-RAY DIFFRACTIONr_chiral_restr0.0810.2850
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216078
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021141
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.6894.292779
X-RAY DIFFRACTIONr_mcbond_other4.6894.292778
X-RAY DIFFRACTIONr_mcangle_it4.6786.363481
X-RAY DIFFRACTIONr_mcangle_other4.6776.363482
X-RAY DIFFRACTIONr_scbond_it11.2355.3742533
X-RAY DIFFRACTIONr_scbond_other11.2335.3742533
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.9437.5483757
X-RAY DIFFRACTIONr_long_range_B_refined11.5116.8376237
X-RAY DIFFRACTIONr_long_range_B_other11.50916.846238
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 160 -
Rwork0.24 4955 -
obs--96.55 %
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)
10.8929-0.0544-0.44361.49140.54871.77210.07510.08480.0341-0.1783-0.07880.0962-0.1816-0.1150.00370.03530.0219-0.00590.01630.00050.0089-15.3404-2.564128.0926
21.7363-0.0317-0.17711.18240.74361.8306-0.0226-0.0421-0.08160.01680.1029-0.11560.1570.1593-0.08030.04450.0224-0.00470.02-0.01010.01584.4571-27.021812.3361
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 345
2X-RAY DIFFRACTION2B6 - 345

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