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- PDB-4k8l: Crystal structure of a putative 4-hydroxyproline epimerase/3-hydr... -

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Basic information

Entry
Database: PDB / ID: 4k8l
TitleCrystal structure of a putative 4-hydroxyproline epimerase/3-hydroxyproline dehydratse from the soil bacterium ochrobacterium anthropi, target efi-506495, disordered loops
ComponentsProline racemase
KeywordsISOMERASE / PROLINE RACEMASE / PROPOSED 3-OH PROLINE DEHYDRATASE / EFI / ENZYME FUNCTION INTIATIVE / Structural Genomics / Enzyme Function Initiative
Function / homology4-hydroxyproline epimerase / 4-hydroxyproline epimerase activity / Proline racemase family / Proline racemase / Diaminopimelate Epimerase; Chain A, domain 1 / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha Beta / 4-hydroxyproline 2-epimerase 1
Function and homology information
Biological speciesOchrobactrum anthropi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsVetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Scott Glen, A. ...Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Scott Glen, A. / Chowdhury, S. / Evens, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal structure of a putative 4-hydroxyproline epimerase/3-hydroxyproline dehydratse from the soil bacterium ochrobacterium anthropi, target efi-506495, disordered loops
Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Scott Glen, A. / Chowdhury, S. / Evens, B. / Hammonds, ...Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Scott Glen, A. / Chowdhury, S. / Evens, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionApr 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Structure summary
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proline racemase


Theoretical massNumber of molelcules
Total (without water)37,0281
Polymers37,0281
Non-polymers00
Water3,441191
1
A: Proline racemase

A: Proline racemase


Theoretical massNumber of molelcules
Total (without water)74,0572
Polymers74,0572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area2860 Å2
ΔGint-14 kcal/mol
Surface area24810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.263, 78.329, 114.424
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-430-

HOH

21A-533-

HOH

31A-535-

HOH

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Components

#1: Protein Proline racemase


Mass: 37028.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ochrobactrum anthropi (bacteria) / Strain: ATCC 49188 / Gene: Oant_0439 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A6WW16
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O

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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: 2.34 Å3/Da / Density % sol: 47.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein (15 mM Hepes, Reservoir MCSG2-C10 (0.2 M Sodium Nitrate, 20 %(w/v) PEG 3350) Cryoprotection (Reservoir+20% glycerol), pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 25, 2012 / 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: 1.9→64.635 Å / Num. all: 27674 / Num. obs: 27674 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 11.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-27.30.5941.32889039810.594100
2-2.127.30.38322750537810.383100
2.12-2.277.30.25532610435840.255100
2.27-2.457.30.1864.12405833060.186100
2.45-2.697.30.1325.52242930830.132100
2.69-37.30.10862033727910.108100
3-3.477.30.096.81801224830.09100
3.47-4.257.20.0679.31514420970.067100
4.25-6.017.10.041141188016690.041100
6.01-28.6066.50.03617.258498990.03694.9

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TM0

1tm0


Resolution: 1.9→28.606 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8627 / SU ML: 0.17 / σ(F): 0 / σ(I): 0 / Phase error: 20.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2071 1391 5.03 %RANDOM
Rwork0.1654 ---
all0.1675 27671 --
obs0.1675 27671 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.12 Å2 / Biso mean: 34.0144 Å2 / Biso min: 7.46 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28.606 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2282 0 0 191 2473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112324
X-RAY DIFFRACTIONf_angle_d1.3493148
X-RAY DIFFRACTIONf_chiral_restr0.08364
X-RAY DIFFRACTIONf_plane_restr0.008412
X-RAY DIFFRACTIONf_dihedral_angle_d13.031860
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.96790.22611310.207725792710100
1.9679-2.04670.21731390.175626122751100
2.0467-2.13980.24771410.161826072748100
2.1398-2.25260.19511220.152526072729100
2.2526-2.39360.22161390.146826252764100
2.3936-2.57830.17381400.15126002740100
2.5783-2.83760.21811570.156926112768100
2.8376-3.24770.20111550.158126232778100
3.2477-4.08980.20211200.167726962816100
4.0898-28.60920.20761470.17512720286798
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)
11.7093-0.13760.17521.8679-0.49051.5239-0.01430.12230.1128-0.08090.01980.0985-0.0939-0.0744-0.01550.130.0004-0.01540.09640.02210.093433.375415.044746.7239
21.9705-0.21240.61910.5488-0.08753.15080.07041.10010.311-0.3464-0.2235-0.3663-0.30531.06620.06560.31810.08640.00640.56740.14970.23632.71823.190921.8278
31.57640.4939-0.09640.52320.17441.0740.26030.2904-0.2853-0.2675-0.04830.1490.34120.068-0.19630.33970.0951-0.10030.29690.02590.294919.133918.423825.8548
40.6737-0.42210.3520.9571-0.22030.6817-0.06990.10820.2979-0.20050.0187-0.0672-0.1354-0.0201-0.01150.1974-0.0163-0.02290.12220.05770.21631.60114.609240.6798
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 142 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 143 through 222 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 223 through 280 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 289 through 332 )A0

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