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- PDB-4juu: Crystal structure of a putative hydroxyproline epimerase from xan... -

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Basic information

Entry
Database: PDB / ID: 4juu
TitleCrystal structure of a putative hydroxyproline epimerase from xanthomonas campestris (TARGET EFI-506516) with bound phosphate and unknown ligand
ComponentsEpimeraseEpimerase and racemase
KeywordsISOMERASE / 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 / Unknown ligand / 4-hydroxyproline 2-epimerase
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (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. / 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 a putative hydroxyproline epimerase from xanthomonas campestris (TARGET EFI-506516) with bound phosphate and unknown ligand
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
DepositionMar 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 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 / 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 / _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: Epimerase
B: Epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1179
Polymers70,6072
Non-polymers5107
Water10,737596
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-56 kcal/mol
Surface area24090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.893, 108.749, 116.204
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Epimerase / Epimerase and racemase


Mass: 35303.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Strain: campestris str. ATCC 33913 / Gene: XCC2415 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8P833
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 596 / 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: 2.46 Å3/Da / Density % sol: 49.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein (15 mM Hepes pH 8.0, 150 mM NaCl, 5% glycerol, 10 mM 4OH-PROLINE), Reservoir (0.1 M HEPES pH 7.5, 0.8 M Sodium Phosphate, 0.8 M Potassium Phosphate), Soak 2 minutes in (Reservoir + ...Details: Protein (15 mM Hepes pH 8.0, 150 mM NaCl, 5% glycerol, 10 mM 4OH-PROLINE), Reservoir (0.1 M HEPES pH 7.5, 0.8 M Sodium Phosphate, 0.8 M Potassium Phosphate), Soak 2 minutes in (Reservoir + 20% Glycerol), 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 MX225HE / Detector: CCD / Date: Mar 6, 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: 1.75→79.402 Å / Num. all: 70700 / Num. obs: 70700 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 18
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.75-1.847.10.7251.172237101690.72599.4
1.84-1.967.20.4591.76959596430.45999.7
1.96-2.097.30.2662.96631690520.26699.7
2.09-2.267.40.1764.36262984930.17699.8
2.26-2.477.40.1226.35792678650.12299.9
2.47-2.777.40.0868.85244871210.08699.9
2.77-3.27.30.055124628463140.055100
3.2-3.917.30.03816.83919054040.03899.9
3.91-5.537.10.02921.53021142390.02999.9

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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: PDB entry 4JBD

4jbd


Resolution: 1.75→30.388 Å / Occupancy max: 1 / Occupancy min: 0.36 / FOM work R set: 0.8896 / SU ML: 0.15 / σ(F): 0 / σ(I): 0 / Phase error: 17.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1842 3569 5.05 %RANDOM
Rwork0.152 ---
all0.1536 70611 --
obs0.1536 70611 99.57 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.89 Å2 / Biso mean: 26.7968 Å2 / Biso min: 9.22 Å2
Refinement stepCycle: LAST / Resolution: 1.75→30.388 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4622 0 37 596 5255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014785
X-RAY DIFFRACTIONf_angle_d1.266519
X-RAY DIFFRACTIONf_chiral_restr0.079709
X-RAY DIFFRACTIONf_plane_restr0.006876
X-RAY DIFFRACTIONf_dihedral_angle_d12.241683
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.7740.26421580.21552636279499
1.774-1.79930.24011320.2042592272499
1.7993-1.82620.27481470.18742670281799
1.8262-1.85470.22591280.18062636276499
1.8547-1.88510.23331340.17962663279799
1.8851-1.91760.21451340.16792637277199
1.9176-1.95250.20351440.16432660280499
1.9525-1.990.23471320.159726552787100
1.99-2.03060.21281560.15126562812100
2.0306-2.07480.16211280.13792663279199
2.0748-2.1230.19091300.135726722802100
2.123-2.17610.15871480.128426612809100
2.1761-2.23490.16771420.13526362778100
2.2349-2.30070.17071420.139626952837100
2.3007-2.37490.17481280.13226942822100
2.3749-2.45970.191450.136926552800100
2.4597-2.55820.1831380.147426842822100
2.5582-2.67450.17181350.146427032838100
2.6745-2.81540.21481370.149926952832100
2.8154-2.99170.18161500.160927072857100
2.9917-3.22250.16991650.151127082873100
3.2225-3.54630.16931620.151426962858100
3.5463-4.05840.14831340.139427482882100
4.0584-5.10920.15561550.127227692924100
5.1092-30.3880.22081650.19642851301698
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)
11.4981-0.3899-0.56240.960.20281.7639-0.086-0.1279-0.06630.1260.07050.03060.19590.00880.01650.1783-0.0004-0.00090.10840.02650.12128.5189-3.984626.8918
21.52310.9579-0.52732.481-0.42382.7595-0.0238-0.12610.05560.191-0.0091-0.112-0.26450.14470.03280.14280.039-0.02370.15350.01680.16066.76722.120521.9535
32.185-1.2149-0.47322.02570.37871.2576-0.0789-0.13750.00610.18030.06030.20310.0157-0.15780.02950.1353-0.01890.00280.1440.03440.10042.51776.015121.8219
41.9896-0.1857-0.27640.76540.12651.93480.00910.1373-0.0743-0.078-0.00960.00790.1443-0.0366-0.00950.1447-0.0053-0.00380.0964-0.00520.113818.3057-6.6236-4.5308
50.8150.0587-0.53013.377-1.27452.71970.03540.00620.075-0.11110.01170.0299-0.03660.0353-0.05430.0729-0.01-0.00950.12180.00210.15132.177515.04020.07
62.6770.3127-0.73081.5897-0.31531.0721-0.0470.2601-0.1264-0.2373-0.026-0.27530.11320.04350.09180.18060.02420.00650.1356-0.00810.085727.7669-0.9506-0.0192
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 136 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 137 through 251 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 252 through 312 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 136 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 137 through 251 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 252 through 312 )B0

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