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- PDB-1c5f: CRYSTAL STRUCTURE OF THE CYCLOPHILIN-LIKE DOMAIN FROM BRUGIA MALA... -

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Basic information

Entry
Database: PDB / ID: 1c5f
TitleCRYSTAL STRUCTURE OF THE CYCLOPHILIN-LIKE DOMAIN FROM BRUGIA MALAYI COMPLEXED WITH CYCLOSPORIN A
Components
  • CYCLOSPORIN A
  • PEPTIDYL-PROLYL CIS-TRANS ISOMERASE 1
KeywordsISOMERASE/IMMUNOSUPPRESSANT / ISOMERASE-IMMUNOSUPPRESSANT COMPLEX / CYCLOPHILIN-CYCLOSPORIN COMPLEX / CYCLOSPORIN A / IMMUNOSUPPRESSANT / CYCLOPHILIN
Function / homology
Function and homology information


cyclosporin A binding / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / protein folding / mitochondrion
Similarity search - Function
Cyclophilin-like / Cyclophilin / 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
Cyclosporin A / : / Peptidyl-prolyl cis-trans isomerase 1
Similarity search - Component
Biological speciesBRUGIA MALAYI (agent of lymphatic filariasis)
TOLYPOCLADIUM INFLATUM (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsEllis, P.J. / Carlow, C.K.S. / Ma, D. / Kuhn, P.
CitationJournal: Biochemistry / Year: 2000
Title: Crystal Structure of the Complex of Brugia Malayi Cyclophilin and Cyclosporin A.
Authors: Ellis, P.J. / Carlow, C.K. / Ma, D. / Kuhn, P.
History
DepositionNov 22, 1999Deposition site: RCSB / Processing site: RCSB
SupersessionDec 2, 1999ID: 1QTL
Revision 1.0Dec 3, 1999Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.4Dec 12, 2012Group: Other
Revision 1.5Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name
Revision 1.6Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_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 1
B: CYCLOSPORIN A
C: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE 1
D: CYCLOSPORIN A
E: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE 1
F: CYCLOSPORIN A
G: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE 1
H: CYCLOSPORIN A
I: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE 1
J: CYCLOSPORIN A
K: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE 1
L: CYCLOSPORIN A
M: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE 1
N: CYCLOSPORIN A
O: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE 1
P: CYCLOSPORIN A


Theoretical massNumber of molelcules
Total (without water)165,80016
Polymers165,80016
Non-polymers00
Water6,071337
1
A: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE 1
B: CYCLOSPORIN A


Theoretical massNumber of molelcules
Total (without water)20,7252
Polymers20,7252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-8 kcal/mol
Surface area8510 Å2
MethodPISA
2
C: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE 1
D: CYCLOSPORIN A


Theoretical massNumber of molelcules
Total (without water)20,7252
Polymers20,7252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-8 kcal/mol
Surface area8360 Å2
MethodPISA
3
E: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE 1
F: CYCLOSPORIN A


Theoretical massNumber of molelcules
Total (without water)20,7252
Polymers20,7252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-7 kcal/mol
Surface area8420 Å2
MethodPISA
4
G: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE 1
H: CYCLOSPORIN A


Theoretical massNumber of molelcules
Total (without water)20,7252
Polymers20,7252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-8 kcal/mol
Surface area8100 Å2
MethodPISA
5
I: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE 1
J: CYCLOSPORIN A


Theoretical massNumber of molelcules
Total (without water)20,7252
Polymers20,7252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-8 kcal/mol
Surface area8150 Å2
MethodPISA
6
K: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE 1
L: CYCLOSPORIN A


Theoretical massNumber of molelcules
Total (without water)20,7252
Polymers20,7252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-8 kcal/mol
Surface area8330 Å2
MethodPISA
7
M: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE 1
N: CYCLOSPORIN A


Theoretical massNumber of molelcules
Total (without water)20,7252
Polymers20,7252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-8 kcal/mol
Surface area8310 Å2
MethodPISA
8
O: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE 1
P: CYCLOSPORIN A


Theoretical massNumber of molelcules
Total (without water)20,7252
Polymers20,7252
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-8 kcal/mol
Surface area8170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.000, 100.160, 133.920
Angle α, β, γ (deg.)90.00, 93.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PEPTIDYL-PROLYL CIS-TRANS ISOMERASE 1 / E.C.5.2.1.8 / PPIASE 1 / ROTAMASE / CYCLOPHILIN


Mass: 19504.418 Da / Num. of mol.: 8 / Fragment: CYCLOPHILIN-LIKE DOMAIN, RESIDUES 1-177
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BRUGIA MALAYI (agent of lymphatic filariasis)
Gene: BMCYP-1 / Plasmid: PMAL-C2 / Gene (production host): MBP FUSION PROTEIN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ER2267 / References: UniProt: Q27450, peptidylprolyl isomerase
#2: Protein/peptide
CYCLOSPORIN A / CYCLOSPORINE / CICLOSPORIN / CICLOSPORINE


Type: Cyclic peptide / Class: Immunosuppressant / Mass: 1220.625 Da / Num. of mol.: 8 / Source method: obtained synthetically
Details: CYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. CYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI.
Source: (synth.) TOLYPOCLADIUM INFLATUM (fungus) / References: NOR: NOR00033, Cyclosporin A
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. HERE, CYCLOSPORIN A IS REPRESENTED BY THE SEQUENCE (SEQRES)

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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: 2.5 Å3/Da / Density % sol: 50.83 %
Crystal growpH: 6 / Details: PEG 8000, CALCIUM ACETATE, METHANOL, MES, PH 6.00
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
220 %(w/v)PEG80001reservoir
30.4 Mcadmium acetate1reservoir
40.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 4, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.47→47.14 Å / Num. obs: 56200 / % possible obs: 95.7 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 53.4 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9
Reflection shellResolution: 2.47→2.53 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.372 / % possible all: 73.1
Reflection
*PLUS
% possible obs: 77.5 % / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Num. measured all: 409247 / Rmerge(I) obs: 0.12

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Processing

Software
NameVersionClassification
AMoREphasing
CNSrefinement
MAR345data collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.47→47.1 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: USED MAXIMUM LIKELIHOOD TARGET BASED ON STRUCTURE FACTORS WITH NO CUTOFFS
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2845 5.06 %RANDOM
Rwork0.201 ---
obs0.201 56200 95.1 %-
Solvent computationBsol: 31.56 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso mean: 43.46 Å2
Baniso -1Baniso -2Baniso -3
1--13.823 Å20 Å26.038 Å2
2--3.648 Å20 Å2
3---10.175 Å2
Refinement stepCycle: LAST / Resolution: 2.47→47.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11437 0 0 337 11774
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.32
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it2.032
X-RAY DIFFRACTIONc_scbond_it1.822
X-RAY DIFFRACTIONc_scangle_it2.642.5
LS refinement shellResolution: 2.47→2.58 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3733 285 4.92 %
Rwork0.3172 5791 -
obs--79.17 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 47.1 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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