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- PDB-4j9w: Crystal structure of the complex of a hydroxyproline epimerase (T... -

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Basic information

Entry
Database: PDB / ID: 4j9w
TitleCrystal structure of the complex of a hydroxyproline epimerase (TARGET EFI-506499, PSEUDOMONAS FLUORESCENS PF-5) with the inhibitor pyrrole-2-carboxylate
ComponentsProline racemase family protein
KeywordsIsomerase/Isomerase Inhibitor complex / EPIMERASE / PUTATIVE HYDROXYPROLINE EPIMERASE / enzyme function initiative / EFI / Structural Genomics / Isomerase-Isomerase Inhibitor complex complex
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
PYRROLE-2-CARBOXYLATE / 4-hydroxyproline 2-epimerase
Similarity search - Component
Biological speciesPseudomonas protegens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsVetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. ...Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Stead, M. / 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 the complex of a hydroxyproline epimerase (TARGET EFI-506499, PSEUDOMONAS FLUORESCENS PF-5) with the inhibitor pyrrole-2-carboxylate
Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Stead, ...Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Stead, M. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionFeb 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)72,6239
Polymers72,0812
Non-polymers5427
Water9,674537
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-19 kcal/mol
Surface area23160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.174, 74.637, 87.048
Angle α, β, γ (deg.)90.000, 105.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Proline racemase family protein


Mass: 36040.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas protegens (bacteria) / Strain: Pf-5 / Gene: PFL_1412 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4KGU2
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PYC / PYRROLE-2-CARBOXYLATE


Mass: 110.091 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H4NO2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 537 / 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: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal growTemperature: 298 K / Method: sitting drop vapor diffuction / pH: 5.6
Details: Protein (15 mM Hepes pH 8.0, 150 mM NaCl, 5% glycerol, 20 mM PYRROLE-2-CARBOXYLATE), Reservoir (0.17 M Ammonium Acetate, 0.085 M Sodium Citrate pH 5.6, 25.5 %(w/v) PEG 4000, 15 %(v/v) ...Details: Protein (15 mM Hepes pH 8.0, 150 mM NaCl, 5% glycerol, 20 mM PYRROLE-2-CARBOXYLATE), Reservoir (0.17 M Ammonium Acetate, 0.085 M Sodium Citrate pH 5.6, 25.5 %(w/v) PEG 4000, 15 %(v/v) Glycerol), Soak 2 minutes in (Reservoir + 20% Ethylene Glycol, 20 mM PYRROLE-2-CARBOXYLATE), sitting drop vapor diffuction, 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 MX225HE / Detector: CCD / Date: Feb 14, 2013 / 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: 1.6→83.898 Å / Num. all: 90740 / Num. obs: 90740 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 6.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.6-1.693.50.4341.746795131960.43499.5
1.69-1.793.60.2972.544794125360.29799.4
1.79-1.913.60.2193.242150118000.21999.6
1.91-2.073.60.1514.438949109020.15199.4
2.07-2.263.60.1115.736023100860.11199.4
2.26-2.533.60.0976.13298791830.09799.8
2.53-2.923.70.0935.82987781450.093100
2.92-3.583.70.0737.12537368520.07399.9
3.58-5.063.70.0688.11926452670.06898.6
5.06-26.1883.50.0836.7975927730.08393

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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: PDB entry 2AZP

2azp


Resolution: 1.6→26.188 Å / Occupancy max: 1 / Occupancy min: 0.29 / FOM work R set: 0.7835 / SU ML: 0.16 / σ(F): 0 / σ(I): 0 / Phase error: 27.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2318 4552 5.02 %RANDOM
Rwork0.1967 ---
all0.1985 90665 --
obs0.1985 90665 99.24 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.52 Å2 / Biso mean: 22.2842 Å2 / Biso min: 6.23 Å2
Refinement stepCycle: LAST / Resolution: 1.6→26.188 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4708 0 36 537 5281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064855
X-RAY DIFFRACTIONf_angle_d1.0796585
X-RAY DIFFRACTIONf_chiral_restr0.078718
X-RAY DIFFRACTIONf_plane_restr0.006874
X-RAY DIFFRACTIONf_dihedral_angle_d14.7471748
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.61820.33831390.28862864300399
1.6182-1.63720.31981280.26742899302799
1.6372-1.65720.29831560.26652843299999
1.6572-1.67820.31421420.25592869301199
1.6782-1.70020.28051530.24242879303299
1.7002-1.72350.29831700.232127992969100
1.7235-1.74810.22881580.22482878303699
1.7481-1.77420.26541670.2122857302499
1.7742-1.80190.2791320.219428672999100
1.8019-1.83150.24031500.21092860301099
1.8315-1.86310.23281550.20212868302399
1.8631-1.89690.23941570.19932865302299
1.8969-1.93340.19221320.19332893302599
1.9334-1.97280.22771690.18882831300099
1.9728-2.01570.22311480.19422868301699
2.0157-2.06260.21951460.188828693015100
2.0626-2.11420.22951430.19362872301599
2.1142-2.17130.25931490.19122876302599
2.1713-2.23520.26231460.18928663012100
2.2352-2.30730.25481450.187428833028100
2.3073-2.38970.19741550.185429003055100
2.3897-2.48530.23831450.206528883033100
2.4853-2.59830.25871680.200928733041100
2.5983-2.73510.2621680.203328833051100
2.7351-2.90630.25921680.194528833051100
2.9063-3.13040.21841680.193329023070100
3.1304-3.44480.19981460.177928993045100
3.4448-3.94180.20111620.18229053067100
3.9418-4.96070.20431560.17362866302298
4.9607-26.1880.23271310.21372808293994
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)
10.5982-0.255-0.11941.2456-0.02730.9115-0.05640.11760.1644-0.07080.0042-0.1088-0.28210.30160.030.1133-0.0710.01160.15990.02470.132822.537425.301516.8055
20.6212-0.07240.17320.93010.33511.2213-0.08650.07250.1919-0.1348-0.01890.044-0.30030.160.07860.1574-0.0407-0.02270.11750.02270.14317.089330.628918.125
30.8839-0.3357-0.15981.8714-1.14440.8646-0.144-0.07610.19250.29360.0551-0.4327-0.29830.4251-0.05130.1083-0.0494-0.05330.2022-0.03460.193829.227127.337130.5102
40.5591-0.00660.17970.50990.09990.6464-0.0382-0.0407-0.0315-0.1024-0.15960.2921-0.0778-0.37640.10540.14060.0186-0.02410.2543-0.13350.27042.759733.034539.6947
50.6562-0.05420.5971.15550.44820.9703-0.1617-0.07240.0437-0.0883-0.14740.2524-0.0737-0.49510.14680.15970.01560.00430.2242-0.08010.1663.353928.232438.4624
62.00480.51550.32422.52130.59282.7124-0.26760.18690.1405-0.2529-0.26330.5501-0.2052-0.6449-0.63760.196-0.0356-0.04770.4426-0.16790.3003-3.079922.543331.5193
70.8777-0.6271-0.06941.0382-0.02451.32360.02770.10990.297-0.1909-0.29440.2038-0.3681-0.45830.16310.25050.0722-0.07020.2311-0.07330.25562.911533.398633.7122
80.50480.122-0.16410.90731.02121.3315-0.0366-0.0615-0.00510.1339-0.06840.08190.2645-0.17030.05490.1684-0.01510.00720.1013-0.02160.114910.930924.0841.1209
90.9123-0.6522-0.06662.40980.89050.94330.0287-0.070.22860.18490.1553-0.2495-0.14450.2825-0.10450.2128-0.0252-0.02350.1317-0.04310.169220.083432.310742.94
101.09660.16681.26031.30040.03421.8423-0.02860.01020.069-0.24260.0580.0341-0.06570.1646-0.04670.0635-0.00130.03870.11780.01180.090416.699518.602610.7522
110.9862-0.10240.20391.1818-0.59590.53670.05270.1057-0.1238-0.15150.0336-0.0920.2030.27860.21550.08190.05750.02640.1618-0.04350.108721.56452.35914.2565
120.7940.42360.29380.9220.13531.34780.02430.0125-0.14970.0473-0.0082-0.03510.25810.109-0.02250.10850.04190.01640.1003-0.010.112216.7574-3.228916.9741
130.85090.58230.83591.22580.40541.0815-0.01290.0166-0.0081-0.09050.01380.07910.0932-0.06250.00040.10690.00680.02020.0909-0.01470.09123.3136-1.77376.0554
141.5116-0.16350.21611.89250.88880.87270.0332-0.5350.40140.5037-0.08580.09730.1474-0.2387-0.06540.2234-0.02290.01820.4265-0.1670.2312-7.05714.974520.9397
151.46960.27660.39831.2902-0.47921.53250.0205-0.4091-0.16570.069-0.2061-0.03490.2939-0.20380.13360.1918-0.07780.02610.20570.00380.1607-4.2199-5.869815.2375
160.94440.54090.29020.96330.73380.6613-0.1519-0.0680.2464-0.1622-0.03530.1906-0.1335-0.13740.11760.1510.0092-0.03610.0964-0.02660.1531-3.4493.49384.3904
170.90640.96040.05741.99380.14440.6244-0.04350.2092-0.2118-0.21960.0999-0.04010.08050.1643-0.00520.2128-0.0069-0.04130.1278-0.03950.15632.0163-4.3858-3.2277
180.5452-0.30020.74710.891-0.13542.9038-0.01190.0768-0.10130.08150.0512-0.060.10790.1729-0.02150.06540.00240.01390.11180.00510.123521.4188.9922.7055
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 30 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 88 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 89 through 128 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 129 through 154 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 155 through 175 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 176 through 196 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 197 through 213 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 214 through 267 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 268 through 287 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 288 through 310 )A0
11X-RAY DIFFRACTION11chain 'B' and (resid 1 through 30 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 31 through 88 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 89 through 175 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 176 through 196 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 197 through 213 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 214 through 267 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 268 through 287 )B0
18X-RAY DIFFRACTION18chain 'B' and (resid 288 through 310 )B0

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