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- PDB-4dz3: Crystal structure of a Peptidyl-prolyl cis-trans isomerase with s... -

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Basic information

Entry
Database: PDB / ID: 4dz3
TitleCrystal structure of a Peptidyl-prolyl cis-trans isomerase with surface mutation M61H from Burkholderia pseudomallei complexed with FK506
ComponentsPeptidyl-prolyl cis-trans isomerase
KeywordsISOMERASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / metal ion binding
Similarity search - Function
Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Antimicrob.Agents Chemother. / Year: 2014
Title: A structural biology approach enables the development of antimicrobials targeting bacterial immunophilins.
Authors: Begley, D.W. / Fox, D. / Jenner, D. / Juli, C. / Pierce, P.G. / Abendroth, J. / Muruthi, M. / Safford, K. / Anderson, V. / Atkins, K. / Barnes, S.R. / Moen, S.O. / Raymond, A.C. / Stacy, R. ...Authors: Begley, D.W. / Fox, D. / Jenner, D. / Juli, C. / Pierce, P.G. / Abendroth, J. / Muruthi, M. / Safford, K. / Anderson, V. / Atkins, K. / Barnes, S.R. / Moen, S.O. / Raymond, A.C. / Stacy, R. / Myler, P.J. / Staker, B.L. / Harmer, N.J. / Norville, I.H. / Holzgrabe, U. / Sarkar-Tyson, M. / Edwards, T.E. / Lorimer, D.D.
History
DepositionFeb 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Mar 19, 2014Group: Other
Revision 1.3Sep 13, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,16417
Polymers23,8082
Non-polymers2,35615
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-26 kcal/mol
Surface area11960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.980, 106.580, 107.160
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-304-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Peptidyl-prolyl cis-trans isomerase


Mass: 11904.240 Da / Num. of mol.: 2 / Mutation: M61H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b_A0907 / Gene: BURPS1710b_A0907 / Plasmid: pET28-HisSMT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3JK38, peptidylprolyl isomerase

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Non-polymers , 5 types, 146 molecules

#2: Chemical ChemComp-FK5 / 8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN / K506


Mass: 804.018 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C44H69NO12 / Comment: medication*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.94 Å3/Da / Density % sol: 58.12 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Internal tracking number 226597. JCSG well D10. 0.1M Cacodylate pH 6.5, 200mM Calcium Acetate, 30.0% w/v PEG400, 20% Ethylene Glycol Cryo. BupsA.00130.a.D227 PD00193 25.2mg/ml., vapor ...Details: Internal tracking number 226597. JCSG well D10. 0.1M Cacodylate pH 6.5, 200mM Calcium Acetate, 30.0% w/v PEG400, 20% Ethylene Glycol Cryo. BupsA.00130.a.D227 PD00193 25.2mg/ml., vapor diffusion, sitting drop, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 3, 2012 / Details: mirrors
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→47.72 Å / Num. all: 19417 / Num. obs: 19388 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.87 % / Biso Wilson estimate: 26.545 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.17
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2-2.050.5033.367921407100
2.05-2.110.41446688138399.7
2.11-2.170.33456580134299.9
2.17-2.240.3035.364131306100
2.24-2.310.266.36179124999.9
2.31-2.390.22576037122499.9
2.39-2.480.2047.95887118999.8
2.48-2.580.1729.156251131100
2.58-2.70.14710.454061100100
2.7-2.830.1311.651601048100
2.83-2.980.09914.6491499899.8
2.98-3.160.08416.94648946100
3.16-3.380.05823.14416898100
3.38-3.650.04727.8405283399.9
3.65-40.0431.4375577499.5
4-4.470.03137.23468715100
4.47-5.160.02837.1294961999.7
5.16-6.320.03433.32549543100
6.32-8.940.0334.8197443199.8
8.940.02138.9102225296.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å44.51 Å
Translation2.5 Å44.51 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.004data extraction
XDSdata reduction
RefinementMethod to determine structure: molecular replacement
Starting model: PDB entry 3vaw

3vaw


Resolution: 2→47.72 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.933 / SU B: 6.568 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.168 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES: WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.219 991 5.1 %RANDOM
Rwork0.192 ---
all0.193 19417 --
obs0.193 19360 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.101 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å20 Å2
2---1.21 Å20 Å2
3---1.52 Å2
Refinement stepCycle: LAST / Resolution: 2→47.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 160 131 1920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021843
X-RAY DIFFRACTIONr_bond_other_d0.0040.021214
X-RAY DIFFRACTIONr_angle_refined_deg1.5182.0432503
X-RAY DIFFRACTIONr_angle_other_deg0.99332968
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8865230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.51424.0367
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.93215244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.401159
X-RAY DIFFRACTIONr_chiral_restr0.0640.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212050
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02359
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 67 -
Rwork0.24 1223 -
all-1290 -
obs--100 %
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)
12.25050.1410.54532.32670.53062.74590.1638-0.0518-0.21370.16590.0444-0.11830.10230.1117-0.20820.0238-0.0015-0.02830.0166-0.01040.105635.295825.5666-14.5341
21.2909-0.13820.34021.4383-0.85232.60250.01990.03920.04290.1060.01280.0409-0.1357-0.0731-0.03260.026-0.00080.01220.01160.01350.047214.3556.311-14.1008
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 113
2X-RAY DIFFRACTION2B1 - 113

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