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- PDB-7pb3: Structural and Functional analysis of the Proline Racemase (ProR)... -

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Basic information

Entry
Database: PDB / ID: 7pb3
TitleStructural and Functional analysis of the Proline Racemase (ProR) from the Gram-positive bacterium Acetoanaerobium sticklandii
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
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.841 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
DepositionJul 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1054
Polymers75,8852
Non-polymers2202
Water00
1
AAA: Proline racemase A (AsProR)
hetero molecules

AAA: Proline racemase A (AsProR)
hetero molecules

BBB: Proline racemase A (AsProR)
hetero molecules

BBB: Proline racemase A (AsProR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,2108
Polymers151,7694
Non-polymers4404
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
crystal symmetry operation2_554-x,-y,z-1/21
crystal symmetry operation7_555y,x,-z1
Buried area13000 Å2
ΔGint-50 kcal/mol
Surface area49090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.041, 109.041, 105.163
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Proline racemase A (AsProR)


Mass: 37942.312 Da / Num. of mol.: 2
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 (strain ATCC 12662 / DSM 519 / JCM 1433 / NCIMB 10654) (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 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.52 Å3/Da / Density % sol: 51 %
Description: Initial hits were obtained within a week. Subsequently improved by streak seeding and further optimisation screens around hit condition
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging 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: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2.84→109.1 Å / Num. obs: 9545 / % possible obs: 89.7 % / Redundancy: 12.6 % / Biso Wilson estimate: 109.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.046 / Net I/σ(I): 13.6
Reflection shellResolution: 2.84→3.29 Å / Redundancy: 12.3 % / Rmerge(I) obs: 1.877 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 734 / CC1/2: 0.584 / Rpim(I) all: 0.769 / % possible all: 68.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
STARANISOdata scaling
DIALSdata scaling
MoRDaphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6j7c

6j7c


Resolution: 2.841→77.223 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.884 / WRfactor Rfree: 0.334 / WRfactor Rwork: 0.243 / SU B: 56.225 / SU ML: 0.534 / Average fsc free: 0.754 / Average fsc work: 0.804 / Cross valid method: FREE R-VALUE / ESU R Free: 0.853
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3296 542 5.687 %
Rwork0.2513 8988 -
all0.256 --
obs-9530 61.432 %
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: 126.233 Å2
Baniso -1Baniso -2Baniso -3
1-4.282 Å2-0 Å2-0 Å2
2--4.282 Å2-0 Å2
3----8.564 Å2
Refinement stepCycle: LAST / Resolution: 2.841→77.223 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5172 0 16 0 5188
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0135286
X-RAY DIFFRACTIONr_bond_other_d0.0020.0175072
X-RAY DIFFRACTIONr_angle_refined_deg1.4291.6427136
X-RAY DIFFRACTIONr_angle_other_deg1.0581.57911764
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.7035668
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.87924.828232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.38315956
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5011512
X-RAY DIFFRACTIONr_chiral_restr0.0580.2714
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025928
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021068
X-RAY DIFFRACTIONr_nbd_refined0.2230.21909
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.26416
X-RAY DIFFRACTIONr_nbtor_refined0.1610.22501
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.22601
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2212
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0970.210
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1660.241
X-RAY DIFFRACTIONr_nbd_other0.2010.2201
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1680.27
X-RAY DIFFRACTIONr_mcbond_it1.7418.342678
X-RAY DIFFRACTIONr_mcbond_other1.7418.342677
X-RAY DIFFRACTIONr_mcangle_it2.99612.513344
X-RAY DIFFRACTIONr_mcangle_other2.99612.513345
X-RAY DIFFRACTIONr_scbond_it1.328.492606
X-RAY DIFFRACTIONr_scbond_other1.328.4912607
X-RAY DIFFRACTIONr_scangle_it2.42912.6883791
X-RAY DIFFRACTIONr_scangle_other2.42912.6893792
X-RAY DIFFRACTIONr_lrange_it5.513105.246454
X-RAY DIFFRACTIONr_lrange_other5.513105.2366455
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.841-2.9140.64430.29635X-RAY DIFFRACTION3.3688
2.914-2.9940.45220.24768X-RAY DIFFRACTION6.4635
2.994-3.0810.40840.385129X-RAY DIFFRACTION12.4765
3.081-3.1760.41130.41175X-RAY DIFFRACTION18.2524
3.176-3.280.49140.424239X-RAY DIFFRACTION24.9016
3.28-3.3950.414210.398372X-RAY DIFFRACTION40.3491
3.395-3.5230.527270.378533X-RAY DIFFRACTION59.322
3.523-3.6660.387500.381688X-RAY DIFFRACTION82.5503
3.666-3.8290.386430.34786X-RAY DIFFRACTION95.397
3.829-4.0160.355360.316652X-RAY DIFFRACTION81.8074
4.016-4.2330.36390.28765X-RAY DIFFRACTION99.0148
4.233-4.4890.241390.226705X-RAY DIFFRACTION99.4652
4.489-4.7980.348470.212671X-RAY DIFFRACTION99.446
4.798-5.1820.319440.234628X-RAY DIFFRACTION99.7033
5.182-5.6750.325360.246581X-RAY DIFFRACTION99.5161
5.675-6.3430.324310.271532X-RAY DIFFRACTION99.646
6.343-7.320.436270.254484X-RAY DIFFRACTION99.6101
7.32-8.9560.366310.19408X-RAY DIFFRACTION99.7727
8.956-12.6230.214250.17328X-RAY DIFFRACTION100
12.623-77.2230.32100.25209X-RAY DIFFRACTION99.095
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)
11.474-1.05570.17023.1892-1.71763.8989-0.126-0.2723-0.5605-0.10610.15490.09481.0010.1918-0.02890.31740.07860.08810.07150.04840.60537.889-26.419-14.054
22.1417-0.48370.04873.8855-1.18273.91190.0594-0.0913-1.07580.0895-0.19080.03611.3892-0.04310.13140.6103-0.09790.09390.0776-0.06240.85291.457-25.70330.189
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA1 - 335
2X-RAY DIFFRACTION2ALLBBB1 - 335

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