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- PDB-8a3f: Proline Racemase (ProR) from the Gram-positive bacterium Acetoana... -

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Basic information

Entry
Database: PDB / ID: 8a3f
TitleProline Racemase (ProR) from the Gram-positive bacterium Acetoanaerobium sticklandii from isotropic tetragonal data at 3.15 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: 3.15 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 8, 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)
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 area13110 Å2
ΔGint-45 kcal/mol
Surface area47850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.724, 109.724, 104.990
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 DSM 519 (bacteria)
Strain: ATCC 12662 / DSM 519 / JCM 1433 / NCIMB 10654 / Gene: prdF, CLOST_2228 / Details (production host): 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: 2.08 Å3/Da / Density % sol: 51 %
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: 3.15→109.1 Å / Num. obs: 11620 / % possible obs: 100 % / Redundancy: 11.6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.267 / Rpim(I) all: 0.115 / Net I/σ(I): 6.8
Reflection shellResolution: 3.15→3.37 Å / Redundancy: 12.3 % / Rmerge(I) obs: 3.32 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2048 / CC1/2: 0.457 / Rpim(I) all: 1.335 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7pb3

7pb3


Resolution: 3.15→77.707 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.875 / SU B: 127.441 / SU ML: 0.92 / Cross valid method: FREE R-VALUE / ESU R Free: 0.733
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3301 690 5.957 %
Rwork0.2657 10893 -
all0.27 --
obs-11583 99.965 %
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: 127.154 Å2
Baniso -1Baniso -2Baniso -3
1--0.476 Å20 Å20 Å2
2---0.476 Å20 Å2
3---0.951 Å2
Refinement stepCycle: LAST / Resolution: 3.15→77.707 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_deg1.7181.6427136
X-RAY DIFFRACTIONr_angle_other_deg1.0881.57911764
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.5525668
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.59224.828232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.68815956
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.891512
X-RAY DIFFRACTIONr_chiral_restr0.0810.2714
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025928
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021068
X-RAY DIFFRACTIONr_nbd_refined0.250.22064
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2350.26631
X-RAY DIFFRACTIONr_nbtor_refined0.1720.22527
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.22498
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.230.2157
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0220.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2470.257
X-RAY DIFFRACTIONr_nbd_other0.210.2208
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.150.216
X-RAY DIFFRACTIONr_mcbond_it0.6645.1362678
X-RAY DIFFRACTIONr_mcbond_other0.6645.1362677
X-RAY DIFFRACTIONr_mcangle_it1.1797.7043344
X-RAY DIFFRACTIONr_mcangle_other1.1797.7043345
X-RAY DIFFRACTIONr_scbond_it0.5215.2212606
X-RAY DIFFRACTIONr_scbond_other0.5225.2242607
X-RAY DIFFRACTIONr_scangle_it0.9747.8083791
X-RAY DIFFRACTIONr_scangle_other0.9747.8123792
X-RAY DIFFRACTIONr_lrange_it5.45765.7336590
X-RAY DIFFRACTIONr_lrange_other5.45665.7386591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.2320.424620.415776X-RAY DIFFRACTION100
3.232-3.320.347490.347753X-RAY DIFFRACTION100
3.32-3.4160.395410.381751X-RAY DIFFRACTION100
3.416-3.5210.448380.336735X-RAY DIFFRACTION100
3.521-3.6370.34550.34687X-RAY DIFFRACTION100
3.637-3.7640.374390.302695X-RAY DIFFRACTION100
3.764-3.9060.361490.272660X-RAY DIFFRACTION100
3.906-4.0650.304320.249640X-RAY DIFFRACTION100
4.065-4.2460.2280.2618X-RAY DIFFRACTION100
4.246-4.4530.271350.198596X-RAY DIFFRACTION100
4.453-4.6930.265320.195563X-RAY DIFFRACTION100
4.693-4.9770.302450.235521X-RAY DIFFRACTION100
4.977-5.320.381290.262512X-RAY DIFFRACTION100
5.32-5.7450.327330.281467X-RAY DIFFRACTION100
5.745-6.2920.327270.296439X-RAY DIFFRACTION100
6.292-7.0320.444250.271402X-RAY DIFFRACTION100
7.032-8.1140.442190.241365X-RAY DIFFRACTION100
8-9.9240.249290.212300X-RAY DIFFRACTION100
9.924-13.9780.336150.219254X-RAY DIFFRACTION100
13.978-77.7070.31480.296159X-RAY DIFFRACTION100
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)
11.8715-1.42210.50665.2299-2.46184.6393-0.0144-0.2193-0.6511-0.14830.07950.09991.37910.3087-0.0650.93250.08960.04350.72070.06520.27347.931-26.43-13.961
24.1060.5341-0.36234.7826-0.81875.61-0.0326-0.1908-1.55690.388-0.1503-0.22562.064-0.03260.18281.2695-0.13670.06490.6533-0.00160.60111.481-25.73530.074
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA1 - 335
2X-RAY DIFFRACTION2ALLBBB1 - 335

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