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- PDB-6otv: Crystal structure of putative isomerase EC2056 -

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Basic information

Entry
Database: PDB / ID: 6otv
TitleCrystal structure of putative isomerase EC2056
ComponentsPutative isomerase YbhH
KeywordsISOMERASE / structural genomics / CSGID / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


Isomerases / isomerase activity
Similarity search - Function
PrpF protein / PrpF protein / Diaminopimelate Epimerase; Chain A, domain 1 / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / PHOSPHATE ION / Putative isomerase YbhH
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChang, C. / Evdokimova, E. / Savchenko, A. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal structure of putative isomerase EC2056
Authors: Chang, C. / Evdokimova, E. / Savchenko, A. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative isomerase YbhH
B: Putative isomerase YbhH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,79726
Polymers74,1912
Non-polymers1,60624
Water3,081171
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6750 Å2
ΔGint1 kcal/mol
Surface area27370 Å2
2
A: Putative isomerase YbhH
hetero molecules

B: Putative isomerase YbhH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,79726
Polymers74,1912
Non-polymers1,60624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_564-y,x-y+1,z-1/31
Buried area7980 Å2
ΔGint-17 kcal/mol
Surface area26330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.416, 77.416, 174.266
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Putative isomerase YbhH


Mass: 37095.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ybhH, b0769, JW0752 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AAV8, Isomerases
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 4.08 Å3/Da / Density % sol: 69.83 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.26M sodium phosphate monobasic, 0.14M postassium phosphate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97927 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Nov 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 45725 / % possible obs: 99.8 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.017 / Rrim(I) all: 0.038 / Χ2: 0.905 / Net I/σ(I): 14.4 / Num. measured all: 232618
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.4450.65723290.7830.3250.7350.90499.9
2.44-2.4950.5322640.7890.2640.5940.89999.8
2.49-2.534.60.4222880.8560.2190.4750.9299.1
2.53-2.594.90.35422910.9040.1790.3980.90699.7
2.59-2.645.30.322490.9380.1450.3340.883100
2.64-2.75.30.24422610.9530.1180.2710.913100
2.7-2.775.30.19423490.970.0930.2160.88599.9
2.77-2.855.20.15322780.980.0750.170.89999.7
2.85-2.935.10.11422690.9880.0560.1270.87499.9
2.93-3.0250.08622820.9920.0420.0960.92399.9
3.02-3.134.50.06922710.9930.0360.0780.91599.4
3.13-3.265.20.05622980.9960.0270.0620.952100
3.26-3.415.30.04723030.9960.0220.0521.02799.9
3.41-3.585.30.0422720.9980.0190.0441.07399.9
3.58-3.815.20.03422830.9980.0160.0381.07599.8
3.81-4.14.70.0322840.9980.0150.0341.02299.5
4.1-4.525.40.02822770.9980.0130.0310.993100
4.52-5.175.30.02623140.9980.0120.0290.84899.9
5.17-6.514.90.02322690.9990.0110.0260.65499.7
6.51-505.20.01822940.9990.0090.020.53499.7

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3g7k.pdb

3g7k


Resolution: 2.4→43.902 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 20.22
RfactorNum. reflection% reflection
Rfree0.1998 2344 5.17 %
Rwork0.1764 --
obs0.1776 45381 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 125.75 Å2 / Biso mean: 45.7991 Å2 / Biso min: 13.07 Å2
Refinement stepCycle: final / Resolution: 2.4→43.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5141 0 100 171 5412
Biso mean--61.35 40.73 -
Num. residues----700
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3986-2.44750.33641350.25382360249592
2.4475-2.50070.25971470.23032505265297
2.5007-2.55890.22211480.2162469261798
2.5589-2.62290.25571700.209124962666100
2.6229-2.69380.22891440.20925682712100
2.6938-2.77310.23231480.197725822730100
2.7731-2.86250.26631180.212325662684100
2.8625-2.96480.24451000.192225872687100
2.9648-3.08350.19931600.186624962656100
3.0835-3.22380.24541380.188625652703100
3.2238-3.39370.21761320.183725262658100
3.3937-3.60620.20281420.181625372679100
3.6062-3.88450.20211240.161426002724100
3.8845-4.27520.14651500.149725242674100
4.2752-4.89310.15791520.134125382690100
4.8931-6.16210.18041330.171825292662100
6.1621-43.90960.16231030.158725892692100
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)
11.0759-0.43660.02350.598-0.85161.9030.0110.172-0.06290.2437-0.1027-0.09230.13850.06450.0760.3588-0.1846-0.02850.2978-0.05140.2516-20.405921.7933-1.0825
21.14460.96460.13841.7806-0.14991.0611-0.21830.3455-0.8425-0.4740.2079-0.86280.27020.2661-0.28450.4586-0.14360.15620.3348-0.22380.76315.213928.66999.3646
33.61921.43880.40053.1829-0.10330.8747-0.0953-0.0579-0.32480.02350.1133-0.22740.1176-0.00130.00490.4011-0.1155-0.01030.2672-0.0680.3178-6.225130.200715.6113
41.1134-0.64040.05330.40350.09610.4552-0.00930.0806-0.03360.1467-0.1115-0.0649-0.079-0.2330.07550.3226-0.192-0.00050.33970.00110.2469-25.056226.7906-2.9086
51.2141-0.5344-0.54050.5033-0.39252.1115-0.25270.062-0.01030.02270.1709-0.1047-0.00860.19330.05250.4772-0.1051-0.03390.1805-0.05210.2459-28.4387.949735.3699
60.44560.90940.02382.27160.69440.98540.1781-0.1372-0.33380.4714-0.048-1.09540.1310.2764-0.06630.4726-0.1555-0.23070.32290.04070.6843-23.1683-14.104423.2121
72.66070.6527-0.17744.09820.24260.63040.07470.0963-0.03930.1071-0.0681-0.4727-0.11740.1460.01650.4092-0.1251-0.08830.2488-0.03870.3391-29.791-11.155217.8192
81.0339-0.77590.03390.5849-0.05480.2135-0.21830.0851-0.0114-0.01410.0601-0.0439-0.1448-0.13550.07070.4861-0.1014-0.00550.1758-0.01090.2389-35.71768.315835.3727
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 179 )A7 - 179
2X-RAY DIFFRACTION2chain 'A' and (resid 180 through 273 )A180 - 273
3X-RAY DIFFRACTION3chain 'A' and (resid 274 through 337 )A274 - 337
4X-RAY DIFFRACTION4chain 'A' and (resid 338 through 356 )A338 - 356
5X-RAY DIFFRACTION5chain 'B' and (resid 7 through 150 )B7 - 150
6X-RAY DIFFRACTION6chain 'B' and (resid 151 through 255 )B151 - 255
7X-RAY DIFFRACTION7chain 'B' and (resid 256 through 337 )B256 - 337
8X-RAY DIFFRACTION8chain 'B' and (resid 338 through 356 )B338 - 356

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