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- PDB-3k2c: Crystal structure of peptidyl-prolyl cis-trans isomerase from Enc... -

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Basic information

Entry
Database: PDB / ID: 3k2c
TitleCrystal structure of peptidyl-prolyl cis-trans isomerase from Encephalitozoon cuniculi at 1.9 A resolution
ComponentsPeptidyl-prolyl cis-trans isomerase
KeywordsISOMERASE / SSGCID / NIH / NIAID / SBRI / UW / DECODE / PEPTIDYL-PROLYL CIS-TRANS ISOMERASE / ENCEPHALITOZOON CUNICULI / Cytoplasm / Rotamase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


cyclosporin A binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / cytoplasm
Similarity search - Function
Cyclophilin-like / Cyclophilin / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesEncephalitozoon cuniculi (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSSGCID / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be published
Title: Crystal structure of peptidyl-prolyl cis-trans isomerase from Encephalitozoon cuniculi at 1.9 A resolution
Authors: SSGCID / Abendroth, J. / Edwards, T.E. / Staker, B.
History
DepositionSep 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4May 30, 2018Group: Data collection / Derived calculations / Category: pdbx_struct_assembly / pdbx_struct_assembly_gen
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list
Revision 1.5Sep 6, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_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: Peptidyl-prolyl cis-trans isomerase
B: Peptidyl-prolyl cis-trans isomerase
C: Peptidyl-prolyl cis-trans isomerase
D: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,12910
Polymers85,4564
Non-polymers6736
Water7,891438
1
A: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6043
Polymers21,3641
Non-polymers2402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6043
Polymers21,3641
Non-polymers2402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4602
Polymers21,3641
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4602
Polymers21,3641
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.810, 73.860, 63.590
Angle α, β, γ (deg.)90.01, 79.10, 90.02
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: HOH / End label comp-ID: HOH / Refine code: 6 / Auth seq-ID: 1 - 175 / Label seq-ID: 22

Dom-IDAuth asym-IDLabel asym-ID
1AA - K
2BB - L
3CC - M
4DD - N

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Components

#1: Protein
Peptidyl-prolyl cis-trans isomerase / PPIase / Rotamase / Cyclophilin / CPH


Mass: 21364.074 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Encephalitozoon cuniculi (fungus) / Gene: CPR1, ECU08_0470 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8SRE1, peptidylprolyl isomerase
#2: Chemical ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE


Mass: 178.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / 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: 2.09 Å3/Da / Density % sol: 41.28 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: HAMPTON RESEARCH CRYSTAL SCREEN CONDITION B5: 200mM Li sulfate, 100mM Tris-HCl pH 8.5, 30% PEG 4000; Protein at 49.8 mg/mL, VAPOR DIFFUSION, SITTING DROP, temperature 290.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97351 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97351 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. all: 50563 / Num. obs: 47719 / % possible obs: 94.4 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 26.23 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 11.91
Reflection shellResolution: 1.95→2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 3 / Num. unique all: 50563 / % possible all: 94.7

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Processing

Software
NameVersionClassification
MAR345CCDdata collection
PHASERphasing
REFMAC5.5.0104refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2BIU

2biu


Resolution: 1.95→40 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.93 / SU B: 7.765 / SU ML: 0.1 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.216 2442 5.1 %RANDOM
Rwork0.163 ---
all0.166 47718 --
obs0.166 47718 94.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å2-0.11 Å21.3 Å2
2--1.21 Å2-0 Å2
3----1.15 Å2
Refinement stepCycle: LAST / Resolution: 1.95→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5298 0 42 438 5778
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0215438
X-RAY DIFFRACTIONr_bond_other_d0.0010.023651
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.9447317
X-RAY DIFFRACTIONr_angle_other_deg0.89538869
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7545699
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.29424.146246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.42815858
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3061526
X-RAY DIFFRACTIONr_chiral_restr0.0960.2770
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026201
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021141
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9131.53434
X-RAY DIFFRACTIONr_mcbond_other0.2511.51483
X-RAY DIFFRACTIONr_mcangle_it1.58325435
X-RAY DIFFRACTIONr_scbond_it2.57132004
X-RAY DIFFRACTIONr_scangle_it4.2214.51880
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2045 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Aloose positional0.395
Bloose positional0.395
Cloose positional0.385
Dloose positional0.45
Aloose thermal3.3310
Bloose thermal3.210
Cloose thermal3.1410
Dloose thermal3.3910
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 164 -
Rwork0.223 3342 -
obs--94.58 %
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)
11.08160.0736-0.47670.4424-0.0090.30950.02880.1158-0.05250.0353-0.0523-0.015-0.023-0.07320.02350.00710.0021-0.00380.0949-0.00830.047625.51246.8060.985
20.7842-0.0006-0.44310.47720.01070.29560.0278-0.1138-0.0425-0.0413-0.04850.0154-0.01360.0720.02070.0098-0.0042-0.00180.09770.00150.048325.9799.92510.998
30.2296-0.1146-0.21590.4611-0.10330.5905-0.06290.04590.020.18750.00090.0195-0.01620.0150.0620.1124-0.0210.02290.0606-0.02830.018514.92934.09733.018
40.19620.0213-0.05270.51620.04550.5476-0.0503-0.03230.0046-0.16410.0022-0.0106-0.0275-0.00820.04810.11580.01590.02460.05520.02640.01199.794-2.75841.394
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999

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