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- PDB-4w9r: Crystal structure of uncharacterised protein Coch_1243 from Capno... -

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Basic information

Entry
Database: PDB / ID: 4w9r
TitleCrystal structure of uncharacterised protein Coch_1243 from Capnocytophaga ochracea DSM 7271
ComponentsUncharacterized protein
KeywordsStructural Genomics / Unknown Function / PSI-Biology / Midwest Center for Structural Genomics / MCSG / GEBA
Function / homology
Function and homology information


Esterase-like / Putative esterase / Tetratricopeptide repeat domain / Alpha/Beta hydrolase fold, catalytic domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich ...Esterase-like / Putative esterase / Tetratricopeptide repeat domain / Alpha/Beta hydrolase fold, catalytic domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Esterase
Similarity search - Component
Biological speciesCapnocytophaga ochracea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.703 Å
AuthorsChang, C. / Wu, R. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To Be Published
Title: Crystal structure of uncharacterised protein Coch_1243 from Capnocytophaga ochracea DSM 7271
Authors: Chang, C. / Wu, R. / Clancy, S. / Joachimiak, A.
History
DepositionAug 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Data collection
Revision 1.2Sep 27, 2017Group: Refinement description / Category: software
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,3269
Polymers91,7802
Non-polymers5467
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-12 kcal/mol
Surface area31480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.229, 145.229, 138.391
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Detailsbiological unit is the same as asym.

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Components

#1: Protein Uncharacterized protein


Mass: 45890.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Capnocytophaga ochracea (bacteria) / Strain: ATCC 27872 / DSM 7271 / JCM 12966 / VPI 2845 / Gene: Coch_1243 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: C7M590
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.65 Å3/Da / Density % sol: 73.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.17M Sodium Acetate, 0.085M Tris-Cl, 25.5% PEG4000, 15% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 2, 2013
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 45215 / Num. obs: 45202 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 11.1 % / Biso Wilson estimate: 43.21 Å2 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.038 / Rrim(I) all: 0.11 / Χ2: 0.952 / Net I/av σ(I): 21.641 / Net I/σ(I): 7.1 / Num. measured all: 501033
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.7-2.7510.72.122340.7610.4270.871100
2.75-2.810.722380.8310.3520.87199.9
2.8-2.8510.822710.8480.3310.895100
2.85-2.9110.922350.9330.2520.8881000.7950.834
2.91-2.9710.922570.9160.2160.8951000.6810.714
2.97-3.041122370.9350.1690.9011000.5360.562
3.04-3.121122550.9520.1430.8951000.4530.476
3.12-3.211.122260.9650.1160.9051000.370.388
3.2-3.311.122940.9780.0880.9221000.2820.295
3.3-3.411.222470.9860.0670.9081000.2140.224
3.4-3.5211.222560.9910.0570.9371000.1810.19
3.52-3.6611.322520.9930.0430.9511000.1380.145
3.66-3.8311.322620.9930.0350.9511000.1140.119
3.83-4.0311.322710.9960.031.0181000.0960.1
4.03-4.2911.322630.9960.0251.1251000.080.084
4.29-4.6211.322550.9960.0221.2251000.0720.075
4.62-5.0811.222570.9960.021.1571000.0650.068
5.08-5.811122960.9960.0190.9551000.0610.064
5.81-7.3211.222800.9960.0170.8961000.0530.056
7.32-5011.123160.9980.0120.84799.60.0370.039

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX(phenix.refine: 1.8.3_1479)refinement
PDB_EXTRACT3.15data extraction
SBC-Collectdata collection
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.703→43.309 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.31 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2111 2221 5.03 %Random selection
Rwork0.1836 41914 --
obs0.185 44135 97.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.57 Å2 / Biso mean: 46.8402 Å2 / Biso min: 11.72 Å2
Refinement stepCycle: final / Resolution: 2.703→43.309 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5743 0 36 95 5874
Biso mean--72.02 38.88 -
Num. residues----721
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025953
X-RAY DIFFRACTIONf_angle_d0.6928058
X-RAY DIFFRACTIONf_chiral_restr0.027880
X-RAY DIFFRACTIONf_plane_restr0.0041038
X-RAY DIFFRACTIONf_dihedral_angle_d10.5922218
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7031-2.76190.29911280.25592065219378
2.7619-2.82610.31911360.25832411254791
2.8261-2.89680.30351220.26982615273796
2.8968-2.97510.31511280.25722618274698
2.9751-3.06260.30881380.252659279799
3.0626-3.16150.25491310.242226902821100
3.1615-3.27440.28351450.230926462791100
3.2744-3.40550.24421480.222526802828100
3.4055-3.56040.27181240.21562682280699
3.5604-3.7480.20641380.182626852823100
3.748-3.98270.19381470.16692653280099
3.9827-4.28990.18231440.14126972841100
4.2899-4.72120.13651600.12526632823100
4.7212-5.40320.15631430.129127032846100
5.4032-6.80320.20051480.160926992847100
6.8032-43.31470.16031410.163927482889100
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)
10.009-0.0097-0.01430.01140.0040.0170.0713-0.01210.08540.12720.02410.0566-0.3083-0.09320.12640.60610.13290.1055-0.21020.05450.1396-1.2589114.429211.5017
20.01240.0146-0.00480.02110.00020.00970.0768-0.04790.04380.0815-0.0542-0.0706-0.01420.0270.00570.6673-0.2113-0.06170.10990.00340.252216.7892122.551511.0771
30.01970.0286-0.0450.0382-0.06440.13660.0361-0.16-0.08440.0177-0.0816-0.0837-0.13810.22730.01160.19170.0127-0.04170.17380.07740.237917.784294.538513.5173
40.0354-0.0057-0.01040.06560.01040.0226-0.0336-0.043-0.06920.0722-0.06290.0010.04710.0687-0.07010.20290.1153-0.00280.22190.17810.415314.654271.181521.349
50.0060.00520.00180.0056-0.00210.00580.01320.0585-0.0379-0.0144-0.04330.0502-0.0598-0.05600.3020.0537-0.02040.1284-0.00430.2384-3.0177100.0529-17.0815
60.05630.02110.01550.02120.01390.02110.06980.0914-0.015-0.0114-0.02170.024-0.13810.01260.01750.26240.0726-0.00790.09170.00990.14947.410699.4759-18.5737
70.01560.011-0.00220.01560.01190.01030.12620.04-0.0093-0.0092-0.0275-0.168-0.11920.0732-00.25260.00420.02950.21820.02240.263223.578102.7214-16.0327
80.00030.00050.01650.0134-0.02020.03410.02120.04880.104-0.0647-0.03180.0226-0.04350.0337-0.00490.39390.00130.0712-0.08220.17960.23626.5481131.843-22.1404
90.0051-0.00210.00280.0008-0.00030.00170.03090.02430.0253-0.00060.00480.0409-0.0408-0.0183-00.3268-0.01360.02190.16110.10660.517-7.9057150.6329-24.5712
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 160 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 161 through 232 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 233 through 309 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 310 through 379 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 19 through 61 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 62 through 160 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 161 through 232 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 233 through 344 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 345 through 379 )B0

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