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- PDB-5ez1: Crystal Structure of Cell Binding Factor 2 from Helicobacter pylo... -

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Basic information

Entry
Database: PDB / ID: 5ez1
TitleCrystal Structure of Cell Binding Factor 2 from Helicobacter pylori in complex with I2CA
ComponentsPutative peptidyl-prolyl cis-trans isomerase HP_0175
KeywordsISOMERASE / Cell binding factor 2 / Peptidyl prolyl cis-trans isomerase
Function / homology
Function and homology information


RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase
Similarity search - Function
: / Trigger factor/SurA domain superfamily / Peptidyl-prolyl cis-trans isomerase, PpiC-type, conserved site / PpiC-type peptidyl-prolyl cis-trans isomerase signature. / PPIC-type PPIASE domain / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / Peptidyl-prolyl cis-trans isomerase domain superfamily ...: / Trigger factor/SurA domain superfamily / Peptidyl-prolyl cis-trans isomerase, PpiC-type, conserved site / PpiC-type peptidyl-prolyl cis-trans isomerase signature. / PPIC-type PPIASE domain / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / Peptidyl-prolyl cis-trans isomerase domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
1H-indole-2-carboxylic acid / Putative peptidyl-prolyl cis-trans isomerase HP_0175
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsSun, Y.J. / Chu, C.H. / Tsai, Y.C.
CitationJournal: J.Struct.Biol. / Year: 2016
Title: Helicobacter pylori cell binding factor 2: Insights into domain motion.
Authors: Naveen, V. / Chu, C.H. / Chen, B.W. / Tsai, Y.C. / Hsiao, C.D. / Sun, Y.J.
History
DepositionNov 26, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative peptidyl-prolyl cis-trans isomerase HP_0175
B: Putative peptidyl-prolyl cis-trans isomerase HP_0175
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2614
Polymers63,9392
Non-polymers3222
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-35 kcal/mol
Surface area28680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.998, 61.998, 366.427
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-567-

HOH

21B-507-

HOH

31B-544-

HOH

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Components

#1: Protein Putative peptidyl-prolyl cis-trans isomerase HP_0175 / PPIase HP_0175 / Rotamase HP_0175


Mass: 31969.539 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 33-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria)
Strain: ATCC 700392 / 26695 / Gene: HP_0175 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: P56112, peptidylprolyl isomerase
#2: Chemical ChemComp-ICB / 1H-indole-2-carboxylic acid


Mass: 161.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H7NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 44% Jaffamine M-600 pH 7.0, 50 mM Succinate acid pH 3.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 33151 / % possible obs: 98.9 % / Redundancy: 5.7 % / Net I/σ(I): 30.2

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.4→26.673 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 29.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2995 1530 5.12 %
Rwork0.2442 --
obs0.247 29902 89.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→26.673 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3760 0 24 151 3935
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013846
X-RAY DIFFRACTIONf_angle_d1.2455149
X-RAY DIFFRACTIONf_dihedral_angle_d14.5031523
X-RAY DIFFRACTIONf_chiral_restr0.076556
X-RAY DIFFRACTIONf_plane_restr0.007665
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4005-2.47790.344620.2934929X-RAY DIFFRACTION33
2.4779-2.56640.34531020.28052018X-RAY DIFFRACTION72
2.5664-2.6690.31981410.26272602X-RAY DIFFRACTION93
2.669-2.79040.33161570.26322735X-RAY DIFFRACTION97
2.7904-2.93730.32551540.24572745X-RAY DIFFRACTION97
2.9373-3.12110.29951580.2582744X-RAY DIFFRACTION97
3.1211-3.36170.30111600.2552804X-RAY DIFFRACTION98
3.3617-3.69920.28091670.22342843X-RAY DIFFRACTION99
3.6992-4.23260.27681450.21392870X-RAY DIFFRACTION99
4.2326-5.32570.28921580.21662940X-RAY DIFFRACTION99
5.3257-26.67460.30411260.27633142X-RAY DIFFRACTION99
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)
10.00660.0008-0.00020.00640.00350.00190.01730.0141-0.007-0.01150.0011-0.02-0.00880.0109-0.00010.7374-0.0269-0.08210.65610.19140.630420.277938.964953.2738
20.103-0.02460.12890.22270.03070.1817-0.04580.10950.1766-0.0572-0.066-0.0699-0.08540.03770.03930.44950.15380.0830.24730.10260.380813.207231.823352.3399
30.0146-0.01890.02320.0508-0.02770.08060.01380.03690.0368-0.0202-0.09260.01940.03270.0713-0.0490.39010.13320.12120.2906-0.00830.255228.402210.966946.5527
40.08660.01330.04220.0382-0.00220.0358-0.0585-0.06740.00640.04060.0125-0.06720.03520.0145-0.00620.12490.05840.02180.32970.01240.277445.3352.548820.3616
50.1998-0.081-0.06030.11240.00870.0606-0.1122-0.0977-0.1370.09560.02090.0010.18860.0979-0.2060.13420.26880.21350.0380.03410.246412.7485-3.881-0.2516
60.1756-0.1384-0.04440.10140.03920.012-0.1038-0.1906-0.10510.1047-0.0349-0.18630.18240.3008-0.27650.13140.44190.08120.33780.04220.243219.3506-0.62066.4595
70.0119-0.00320.0240.08570.01050.0771-0.0179-0.0823-0.04680.19080.06140.04880.07990.00720.22140.35350.21730.18460.3160.07650.229838.91111.517336.1516
80.1393-0.1186-0.16430.17540.07580.49850.02070.1262-0.1526-0.0352-0.09830.32060.297-0.1658-0.03280.60540.13150.06480.33190.02890.379620.23799.451950.2026
90.0898-0.06090.06150.0537-0.0190.06120.1809-0.23040.11130.189-0.1119-0.0912-0.1147-0.08750.00010.52440.0450.01890.5805-0.04410.6478-0.677533.40112.4719
100.01560.0033-0.01130.0402-0.00890.0483-0.13130.11140.02060.04630.08910.03980.0498-0.2039-0.00210.5769-0.0028-0.03510.44840.14020.3823-1.796731.439746.05
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 54 through 76 )
2X-RAY DIFFRACTION2chain 'A' and (resid 77 through 103 )
3X-RAY DIFFRACTION3chain 'A' and (resid 104 through 132 )
4X-RAY DIFFRACTION4chain 'A' and (resid 133 through 151 )
5X-RAY DIFFRACTION5chain 'A' and (resid 152 through 196 )
6X-RAY DIFFRACTION6chain 'A' and (resid 197 through 261 )
7X-RAY DIFFRACTION7chain 'A' and (resid 262 through 296 )
8X-RAY DIFFRACTION8chain 'B' and (resid 54 through 132 )
9X-RAY DIFFRACTION9chain 'B' and (resid 133 through 261 )
10X-RAY DIFFRACTION10chain 'B' and (resid 262 through 297 )

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