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- PDB-4dz2: Crystal structure of a Peptidyl-prolyl cis-trans isomerase with s... -

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Basic information

Entry
Database: PDB / ID: 4dz2
TitleCrystal structure of a Peptidyl-prolyl cis-trans isomerase with surface mutation R92G 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
8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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)25,2826
Polymers23,5942
Non-polymers1,6884
Water4,270237
1
A: Peptidyl-prolyl cis-trans isomerase
hetero molecules

A: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2826
Polymers23,5942
Non-polymers1,6884
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2330 Å2
ΔGint-28 kcal/mol
Surface area11540 Å2
MethodPISA
2
B: Peptidyl-prolyl cis-trans isomerase
hetero molecules

B: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2826
Polymers23,5942
Non-polymers1,6884
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2320 Å2
ΔGint-28 kcal/mol
Surface area11610 Å2
MethodPISA
3
A: Peptidyl-prolyl cis-trans isomerase
B: Peptidyl-prolyl cis-trans isomerase
hetero molecules

A: Peptidyl-prolyl cis-trans isomerase
B: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,56512
Polymers47,1894
Non-polymers3,3768
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area7320 Å2
ΔGint-74 kcal/mol
Surface area20480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.440, 49.050, 66.640
Angle α, β, γ (deg.)90.000, 123.050, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase


Mass: 11797.147 Da / Num. of mol.: 2 / Mutation: R92G
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
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 3.09 Å3/Da / Density % sol: 60.19 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Internal tracking number 224744. JCSG well D10. 0.1M Cacodylate pH 6.5, 200mM Calcium Acetate, 30.0% w/v PEG400, 20% Ethylene Glycol Cryo. BupsA.00130.a.D239 PD00214 21.8mg/ml, vapor ...Details: Internal tracking number 224744. JCSG well D10. 0.1M Cacodylate pH 6.5, 200mM Calcium Acetate, 30.0% w/v PEG400, 20% Ethylene Glycol Cryo. BupsA.00130.a.D239 PD00214 21.8mg/ml, vapor diffusion, sitting drop, temperature 290K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→44.61 Å / Num. all: 19744 / Num. obs: 19250 / % possible obs: 97.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.44 % / Biso Wilson estimate: 23.506 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 26.88
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2-2.050.1319.16026139296.6
2.05-2.110.11611.16610139298.5
2.11-2.170.10712.37052136298.3
2.17-2.240.12114.46801129497.1
2.24-2.310.07825.55717111087.8
2.31-2.390.09517.47374114591.6
2.39-2.480.07222.18910121699.7
2.48-2.580.06824.18623117399.4
2.58-2.70.061268094109899.6
2.7-2.830.05528.37926107299.6
2.83-2.980.04731.5738299899.5
2.98-3.160.04134.5724197499.4
3.16-3.380.03639.9667189899.4
3.38-3.650.0443615085099.2
3.65-40.0446.8535576097.7
4-4.470.03248523971898
4.47-5.160.03148.8450161399.7
5.16-6.320.03645388753298.9
6.32-8.940.03645.2297941998.1
8.940.03448.6148723495.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å42.98 Å
Translation2.5 Å42.98 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→44.61 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.913 / SU B: 8.095 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.206 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES: WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.247 950 5.1 %RANDOM
Rwork0.219 ---
all0.22 19744 --
obs0.22 18755 95.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.826 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å20 Å2-0.35 Å2
2--1.09 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 2→44.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1650 0 116 237 2003
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021811
X-RAY DIFFRACTIONr_bond_other_d0.0030.021196
X-RAY DIFFRACTIONr_angle_refined_deg1.4732.0382470
X-RAY DIFFRACTIONr_angle_other_deg0.8932931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6645226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.93724.41268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.7715255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.543159
X-RAY DIFFRACTIONr_chiral_restr0.0710.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212016
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02353
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 70 -
Rwork0.209 1277 -
all-1347 -
obs--96.7 %
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)
11.23250.25060.69750.3750.26111.55890.00450.195-0.13590.06150.14350.0256-0.01810.1604-0.1480.0453-0.00490.00980.091-0.01710.053625.4285-1.18615.6699
21.01050.0747-0.34810.49270.03891.52380.01590.15220.14690.03960.1390.0061-0.0058-0.0926-0.15490.0325-0.00950.00240.07690.03220.061844.654620.003315.549
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 113
2X-RAY DIFFRACTION2B1 - 113

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