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- PDB-4k7x: Crystal structure of a 4-hydroxyproline epimerase from burkholder... -

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Basic information

Entry
Database: PDB / ID: 4k7x
TitleCrystal structure of a 4-hydroxyproline epimerase from burkholderia multivorans, target efi-506479, with bound phosphate, closed domains
ComponentsProline racemase
KeywordsLYASE / PROLINE RACEMASE FAMILY / PROPOSED 4-OH PROLINE EPIMERASE / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
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
PHOSPHATE ION / 4-hydroxyproline 2-epimerase 1
Similarity search - Component
Biological speciesBurkholderia multivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 Glenn, 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 Glenn, A. / Chowdhury, S. / Evans, 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 4-hydroxyproline epimerase from burkholderia multivorans, target efi-506479, with bound phosphate, closed domains
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 Glenn, A. / Chowdhury, S. / Evans, 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 Glenn, A. / Chowdhury, S. / Evans, 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 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 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 / pdbx_struct_special_symmetry / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1209
Polymers35,4951
Non-polymers6258
Water8,341463
1
A: Proline racemase
hetero molecules

A: Proline racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,24118
Polymers70,9902
Non-polymers1,25116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,-y+1/2,-z+1/41
Buried area4930 Å2
ΔGint-88 kcal/mol
Surface area23920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.885, 114.885, 173.699
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-407-

GOL

21A-533-

HOH

31A-633-

HOH

41A-635-

HOH

51A-807-

HOH

61A-895-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Proline racemase


Mass: 35494.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia multivorans (bacteria) / Strain: ATCC 17616 / Gene: prdF, BMULJ_04062 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B3D6W2, proline racemase

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Non-polymers , 5 types, 471 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / 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: 4.04 Å3/Da / Density % sol: 69.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: Protein (10 mM Tris, 150 mM NaCl, 5% glycerol, 5 mM BME, 20 mM pyrrole 2-carboxylate); Reservoir (0.1 M Phosphate-citrate, 1.6 M NaH2PO4/0.4 M K2HPO4 (MCSG2 E10)); Cryoprotection ...Details: Protein (10 mM Tris, 150 mM NaCl, 5% glycerol, 5 mM BME, 20 mM pyrrole 2-carboxylate); Reservoir (0.1 M Phosphate-citrate, 1.6 M NaH2PO4/0.4 M K2HPO4 (MCSG2 E10)); Cryoprotection (Reservoir+20% glycerol), pH 4.2, VAPOR DIFFUSION, HANGING 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 225 HE / Detector: CCD / Date: Apr 6, 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: 1.75→95.823 Å / Num. all: 58608 / Num. obs: 58608 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.3 % / Rmerge(I) obs: 0.13 / Rsym value: 0.13 / Net I/σ(I): 14.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.75-1.8413.50.6991.111379084430.699100
1.84-1.9613.80.4661.611006779960.466100
1.96-2.0914.10.312.410609375510.31100
2.09-2.2614.40.223.410097370110.22100
2.26-2.4714.70.1714.39576664960.171100
2.47-2.7714.80.1484.78763359030.148100
2.77-3.214.80.1324.77764052380.132100
3.2-3.9114.70.0847.66545044390.084100
3.91-5.5314.50.04812.85105735120.048100
5.53-28.77913.70.04114.62768320190.04199.4

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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: 4J9W

4j9w


Resolution: 1.75→28.779 Å / Occupancy max: 1 / Occupancy min: 0.28 / FOM work R set: 0.9253 / SU ML: 0.12 / σ(F): 0 / σ(I): 0 / Phase error: 13.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1564 2964 5.06 %RANDOM
Rwork0.137 ---
all0.138 58574 --
obs0.138 58574 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.89 Å2 / Biso mean: 18.4258 Å2 / Biso min: 6.43 Å2
Refinement stepCycle: LAST / Resolution: 1.75→28.779 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2346 0 33 463 2842
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092491
X-RAY DIFFRACTIONf_angle_d1.2683398
X-RAY DIFFRACTIONf_chiral_restr0.079372
X-RAY DIFFRACTIONf_plane_restr0.007448
X-RAY DIFFRACTIONf_dihedral_angle_d11.742880
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.75-1.77870.18541210.197226032724
1.7787-1.80930.19351430.177526182761
1.8093-1.84220.21591320.164426012733
1.8422-1.87770.17971570.159526212778
1.8777-1.9160.16111370.150626202757
1.916-1.95760.15571380.145126062744
1.9576-2.00320.15481380.143926172755
2.0032-2.05330.16241400.131926662806
2.0533-2.10870.1661400.124525882728
2.1087-2.17080.12991440.122226392783
2.1708-2.24080.13941450.117326052750
2.2408-2.32090.14361520.117526262778
2.3209-2.41380.15361410.120726462787
2.4138-2.52360.15521410.116326542795
2.5236-2.65650.14171330.12526472780
2.6565-2.82280.14941220.129526702792
2.8228-3.04050.15421490.133826522801
3.0405-3.34610.1491620.130826552817
3.3461-3.82930.13831520.127426882840
3.8293-4.82090.13681430.121627252868
4.8209-28.78240.21351340.187428632997
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)
10.49250.24150.15321.6308-0.08231.9289-0.0080.0855-0.0525-0.17240.03890.00730.1364-0.0302-0.02140.0920.0088-0.00150.0787-0.00760.099685.406316.79816.4383
21.1605-0.10590.01940.6401-0.07980.69130.0082-0.0563-0.00220.0004-0.0111-0.04210.09550.07390.00230.10960.0330.0010.0741-0.00120.082498.389110.934333.535
31.03170.1440.4841.0963-0.94936.6304-0.04430.1117-0.0097-0.13320.0841-0.04640.0324-0.0235-0.03190.0881-0.01-0.00560.0171-0.0180.101785.195625.740214.229
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -3 through 60 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 61 through 288 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 289 through 310 )A0

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