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- PDB-8a4r: Proline Racemase (ProR) from the Gram-positive bacterium Acetoana... -

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Basic information

Entry
Database: PDB / ID: 8a4r
TitleProline Racemase (ProR) from the Gram-positive bacterium Acetoanaerobium sticklandii from isotropic orthorhombic data at 3.59 A
ComponentsProline racemase A (AsProR)
KeywordsISOMERASE / pyridoxal 5-phosphate-independent racemase / diaminopimelate epimerase-like (DAPE) fold / stereo inversion / pyrrole 2-carboxylate / Gram-positive bacterium
Function / homologyproline racemase / 4-hydroxyproline epimerase activity / Proline racemase family / Proline racemase / PYRROLE-2-CARBOXYLATE / Proline racemase
Function and homology information
Biological speciesAcetoanaerobium sticklandii DSM 519 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.59 Å
AuthorsNajmudin, S. / Pan, X.-S. / McAuley, K.E. / Fisher, L.M. / Sanderson, M.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/T000848/1 United Kingdom
CitationJournal: To Be Published
Title: Structural and Functional analysis of the Proline Racemase (ProR) from the Gram-positive bacterium Acetoanaerobium sticklandii
Authors: Najmudin, S. / Pan, X.-S. / McAuley, K.E. / Fisher, L.M. / Sanderson, M.R.
History
DepositionJun 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Proline racemase A (AsProR)
BBB: Proline racemase A (AsProR)
CCC: Proline racemase A (AsProR)
DDD: Proline racemase A (AsProR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,9896
Polymers151,7694
Non-polymers2202
Water00
1
AAA: Proline racemase A (AsProR)
BBB: Proline racemase A (AsProR)
hetero molecules

CCC: Proline racemase A (AsProR)

DDD: Proline racemase A (AsProR)


  • defined by author&software
  • 152 kDa, 4 polymers
Theoretical massNumber of molelcules
Total (without water)151,9896
Polymers151,7694
Non-polymers2202
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_544-x,y-1/2,-z-1/21
crystal symmetry operation4_545x+1/2,-y-1/2,-z1
Buried area11920 Å2
ΔGint-45 kcal/mol
Surface area46530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.454, 107.478, 109.052
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Proline racemase A (AsProR)


Mass: 37942.312 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: DSMZ (Leibniz Institute, DSMZ-German Collection of Microorganisms and Cell Cultures GmbH)
Source: (gene. exp.) Acetoanaerobium sticklandii DSM 519 (bacteria)
Strain: ATCC 12662 / DSM 519 / JCM 1433 / NCIMB 10654 / Gene: prdF, CLOST_2228 / Plasmid: pET-29a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): lambdaDE3 pLysS / References: UniProt: E3PTZ4
#2: Chemical ChemComp-PYC / PYRROLE-2-CARBOXYLATE


Mass: 110.091 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H4NO2
Has ligand of interestN

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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: 2.85 Å3/Da / Density meas: 2.47 Mg/m3 / Density % sol: 50 %
Description: Initial hits were obtained within a week. Subsequently improved by further optimisation screens around hit condition with hanging drop vapour diffusion.
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.26 M Ammonium Sulphate, 100 mM Cacodylate, pH 6.5 at rtp

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.59→107.48 Å / Num. obs: 14925 / % possible obs: 100 % / Redundancy: 6.3 % / CC1/2: 0.991 / Rmerge(I) obs: 0.196 / Rpim(I) all: 0.085 / Net I/σ(I): 6.4
Reflection shellResolution: 3.59→3.93 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.015 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3496 / CC1/2: 0.498 / Rpim(I) all: 0.441 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7pb3

7pb3


Resolution: 3.59→76.549 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.835 / Cross valid method: FREE R-VALUE / ESU R Free: 1.125
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3599 747 5.02 %
Rwork0.2597 14134 -
all0.265 --
obs-14881 99.98 %
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: 141.755 Å2
Baniso -1Baniso -2Baniso -3
1-0.996 Å20 Å20 Å2
2--0.124 Å2-0 Å2
3----1.12 Å2
Refinement stepCycle: LAST / Resolution: 3.59→76.549 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10344 0 16 0 10360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01310556
X-RAY DIFFRACTIONr_bond_other_d0.0350.0179976
X-RAY DIFFRACTIONr_angle_refined_deg1.6551.64414252
X-RAY DIFFRACTIONr_angle_other_deg2.3781.57723272
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.77751336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.23324.828464
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.539151912
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1781524
X-RAY DIFFRACTIONr_chiral_restr0.0630.21428
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211700
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021968
X-RAY DIFFRACTIONr_nbd_refined0.2430.23274
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2380.211958
X-RAY DIFFRACTIONr_nbtor_refined0.1680.24928
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.24751
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2339
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.160.217
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2030.269
X-RAY DIFFRACTIONr_nbd_other0.2720.2290
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.240.210
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0340.21
X-RAY DIFFRACTIONr_mcbond_it4.17915.0955356
X-RAY DIFFRACTIONr_mcbond_other4.17915.0965355
X-RAY DIFFRACTIONr_mcangle_it7.14422.6476688
X-RAY DIFFRACTIONr_mcangle_other7.14422.6466689
X-RAY DIFFRACTIONr_scbond_it3.71815.5095200
X-RAY DIFFRACTIONr_scbond_other3.71815.515200
X-RAY DIFFRACTIONr_scangle_it6.52923.1177564
X-RAY DIFFRACTIONr_scangle_other6.52923.1177564
X-RAY DIFFRACTIONr_lrange_it11.281185.61712265
X-RAY DIFFRACTIONr_lrange_other11.281185.61812266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.59-3.6830.47530.4351028X-RAY DIFFRACTION99.8153
3.683-3.7840.433570.371988X-RAY DIFFRACTION100
3.784-3.8930.376550.361962X-RAY DIFFRACTION100
3.893-4.0120.376490.322942X-RAY DIFFRACTION99.8992
4.012-4.1440.332440.317932X-RAY DIFFRACTION100
4.144-4.2890.338280.314899X-RAY DIFFRACTION100
4.289-4.450.371640.275840X-RAY DIFFRACTION100
4.45-4.6310.277470.235826X-RAY DIFFRACTION100
4.631-4.8360.305320.257800X-RAY DIFFRACTION100
4.836-5.0710.329400.247768X-RAY DIFFRACTION100
5.071-5.3440.402560.251712X-RAY DIFFRACTION100
5.344-5.6670.38540.257674X-RAY DIFFRACTION100
5.667-6.0560.316230.268669X-RAY DIFFRACTION100
6.056-6.5370.513290.24618X-RAY DIFFRACTION100
6.537-7.1560.524110.242586X-RAY DIFFRACTION100
7.156-7.9920.369500.201490X-RAY DIFFRACTION100
7.992-9.2120.305230.184460X-RAY DIFFRACTION100
9.212-11.2410.451150.158403X-RAY DIFFRACTION100
11.241-15.7290.251130.203326X-RAY DIFFRACTION100
15.729-76.5490.240.2211X-RAY DIFFRACTION100

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