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- PDB-6hmz: Crystal Structure of a Single-Domain Cyclophilin from Brassica na... -

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Basic information

Entry
Database: PDB / ID: 6hmz
TitleCrystal Structure of a Single-Domain Cyclophilin from Brassica napus Phloem Sap
Components
  • CyclosporinCiclosporin
  • Peptidyl-prolyl cis-trans isomeraseProlyl isomerase
KeywordsISOMERASE / Peptidyl-Prolyl cis/trans Isomerase / Phloem Sap / CYP-like Domain / Cyclophilin Diversity / Cyclosporin A
Function / homology
Function and homology information


cyclosporin A binding / protein peptidyl-prolyl isomerization / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / intracellular membrane-bounded organelle / 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
MALONATE ION / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesBrassica napus (rape)
Tolypocladium inflatum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.98 Å
AuthorsFalke, S. / Hanhart, P. / Garbe, M. / Thiess, M. / Betzel, C. / Kehr, J.
Funding support Germany, 3items
OrganizationGrant numberCountry
European CommissionPCIG14-GA-2013-63 0734 Germany
LFF-GK06 (DELIGRAH) Germany
German Research FoundationDFG KE 856_6-1 Germany
CitationJournal: Sci Rep / Year: 2019
Title: Enzyme activity and structural features of three single-domain phloem cyclophilins from Brassica napus.
Authors: Hanhart, P. / Falke, S. / Garbe, M. / Rose, V. / Thiess, M. / Betzel, C. / Kehr, J.
History
DepositionSep 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Peptidyl-prolyl cis-trans isomerase
A: Cyclosporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7184
Polymers20,5922
Non-polymers1262
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering, SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-15 kcal/mol
Surface area7870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.580, 86.580, 119.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11X-301-

HOH

21X-316-

HOH

31X-346-

HOH

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase / Prolyl isomerase / PPIase


Mass: 19371.025 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brassica napus (rape) / Gene: BnaA09g35540D, GSBRNA2T00037123001 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A078GRH6, peptidylprolyl isomerase
#2: Protein/peptide Cyclosporin / Ciclosporin


Mass: 1220.625 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Tolypocladium inflatum (fungus)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 3.07 Å3/Da / Density % sol: 59.91 %
Description: Bipyramidal crystals grew to a maximum size of approximately 0.2 mm in all three dimensions within three weeks.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: The protein concentration was adjusted to 10 mg/ml. The protein solution was supplemented with cyclosporin A at a molar ratio of 2:1 and mixed with the reservoir solution containing 2.4 M ...Details: The protein concentration was adjusted to 10 mg/ml. The protein solution was supplemented with cyclosporin A at a molar ratio of 2:1 and mixed with the reservoir solution containing 2.4 M sodium malonate, pH 7.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.977→70.12 Å / Num. obs: 16197 / % possible obs: 99.8 % / Redundancy: 5.6 % / Rpim(I) all: 0.046 / Rrim(I) all: 0.112 / Rsym value: 0.101 / Net I/av σ(I): 6.1 / Net I/σ(I): 9.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.98-2.085.90.4661.623300.210.5130.466100
2.08-2.215.60.372222030.1720.4120.372100
2.21-2.365.50.2972.420740.1360.3280.29799.8
2.36-2.555.80.233.119370.1020.2520.2399.9
2.55-2.85.30.18417880.0850.20.1899.9
2.8-3.135.90.1215.816330.0540.1330.121100
3.13-3.615.30.0768.614470.0350.0840.07699.7
3.61-4.425.90.0512.512330.0220.0550.0599.8
4.42-6.255.30.04812.39780.0230.0530.04899.3
6.25-70.125.20.03411.35740.0170.0380.03498.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation36.82 Å2.12 Å

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
MOLREP11.1.00phasing
REFMAC5.8.0103refinement
PDB_EXTRACT3.24data extraction
iMOSFLM7.1.1data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4jjm

4jjm


Resolution: 1.98→70.12 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.747 / SU ML: 0.121 / SU R Cruickshank DPI: 0.1419 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.137
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2231 813 5 %RANDOM
Rwork0.1838 ---
obs0.1856 15368 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 97.8 Å2 / Biso mean: 33.262 Å2 / Biso min: 16.43 Å2
Baniso -1Baniso -2Baniso -3
1-1.68 Å2-0 Å20 Å2
2--1.68 Å2-0 Å2
3----3.36 Å2
Refinement stepCycle: final / Resolution: 1.98→70.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1279 0 93 50 1422
Biso mean--33.81 31.21 -
Num. residues----170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191396
X-RAY DIFFRACTIONr_bond_other_d0.0020.021357
X-RAY DIFFRACTIONr_angle_refined_deg2.0112.0161881
X-RAY DIFFRACTIONr_angle_other_deg1.15733120
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3895169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.62624.28656
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.96815221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.449156
X-RAY DIFFRACTIONr_chiral_restr0.1540.2204
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021601
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02315
LS refinement shellResolution: 1.98→2.031 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 77 -
Rwork0.338 1092 -
all-1169 -
obs--100 %

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