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Basic information

Entry
Database: PDB / ID: 3luo
TitleCrystal Structure and functional characterization of the thermophilic prolyl isomerase and chaperone SlyD
Components
  • Peptidyl-prolyl cis-trans isomeraseProlyl isomerase
  • Suc-Ala-Leu-Pro-Phe-pNA
KeywordsISOMERASE / PROLYL CIS TRANS ISOMERASE / CHAPERONE FUNCTION / TWO DOMAIN PROTEIN / Ni(2+) Zn(2+) BINDING / SLYD
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein refolding / metal ion binding
Similarity search - Function
Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.55 Å
AuthorsLoew, C. / Neumann, P. / Weininger, U. / Stubbs, M.T. / Balbach, J.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal Structure Determination and Functional Characterization of the Metallochaperone SlyD from Thermus thermophilus
Authors: Loew, C. / Neumann, P. / Tidow, H. / Weininger, U. / Haupt, C. / Friedrich-Epler, B. / Scholz, C. / Stubbs, M.T. / Balbach, J.
History
DepositionFeb 18, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2014Group: Derived calculations
Revision 1.3Nov 1, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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: Suc-Ala-Leu-Pro-Phe-pNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2526
Polymers17,9912
Non-polymers2624
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Peptidyl-prolyl cis-trans isomerase
B: Suc-Ala-Leu-Pro-Phe-pNA
hetero molecules

A: Peptidyl-prolyl cis-trans isomerase
B: Suc-Ala-Leu-Pro-Phe-pNA
hetero molecules

A: Peptidyl-prolyl cis-trans isomerase
B: Suc-Ala-Leu-Pro-Phe-pNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,75718
Polymers53,9736
Non-polymers78512
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area6300 Å2
ΔGint-386 kcal/mol
Surface area25740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.400, 111.400, 111.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213

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Components

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


Mass: 17400.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: PET-VECTOR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5SLE7, peptidylprolyl isomerase
#2: Protein/peptide Suc-Ala-Leu-Pro-Phe-pNA


Mass: 590.625 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE PEPTIDE SUBSTRATE WAS PURCHASED FROM A COMPANY.
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 3.2 Å3/Da / Density % sol: 61.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10MG/ML N-SUC-ALA-LEU-PRO-PHE-PNA, 2M AMMONIUM SULFATE, 5 % PEG 400, 100MM MES, PH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 12, 2009 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9841 Å / Relative weight: 1
ReflectionResolution: 2.55→20 Å / Num. all: 7658 / Num. obs: 7636 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.35 % / Biso Wilson estimate: 68.806 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.054 / Net I/σ(I): 23.77
Reflection shellResolution: 2.55→2.65 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 3.5 / Num. measured obs: 5982 / Num. unique all: 808 / Num. unique obs: 808 / Rsym value: 0.662 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
XSCALEdata processing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
MAR345dtbdata collection
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3CGM

3cgm


Resolution: 2.55→19.693 Å / Occupancy max: 1 / Occupancy min: 0.43 / SU ML: 0.33 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.24 / σ(I): 0 / Stereochemistry target values: ML / Details: TLS parameters have been included in refinemnt
RfactorNum. reflection% reflectionSelection details
Rfree0.235 731 5.03 %RANDOM
Rwork0.205 ---
obs0.207 7636 99.93 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 92.506 Å2 / ksol: 0.407 e/Å3
Displacement parametersBiso max: 215.89 Å2 / Biso mean: 94.308 Å2 / Biso min: 31.23 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.33 Å
Luzzati d res low-8 Å
Luzzati sigma a0.37 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.55→19.693 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1160 0 4 21 1185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0231195
X-RAY DIFFRACTIONf_angle_d0.9281614
X-RAY DIFFRACTIONf_chiral_restr0.058174
X-RAY DIFFRACTIONf_plane_restr0.004219
X-RAY DIFFRACTIONf_dihedral_angle_d18.271431
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.55-2.6090.278490.288923972100
2.609-2.6750.391480.28991496299
2.675-2.7470.367480.292923971100
2.747-2.8270.344490.262899948100
2.827-2.9180.264490.225940989100
2.918-3.0220.218480.222913961100
3.022-3.1430.315480.213906954100
3.143-3.2850.151510.1839511002100
3.285-3.4580.239460.163892938100
3.458-3.6730.312500.189936986100
3.673-3.9540.191500.182923973100
3.954-4.3480.21470.16900947100
4.348-4.9690.186490.139928977100
4.969-6.2270.164480.17920968100
6.227-19.6940.225510.254925976100
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)
10.7820.2454-0.0440.47770.36181.77050.3214-0.15750.1354-0.25860.0001-0.2803-0.01610.1942-0.24490.42280.07990.08220.33420.06810.54297.2791-11.9273-19.325
21.5764-0.34750.07061.2920.8771-0.7523-0.0188-0.41420.26690.2252-0.0823-0.2203-0.5473-0.2406-0.14621.42810.2621-0.0071.0020.05021.210719.9229-25.8474-43.2071
32.01054.0425-1.40614.81830.05852.3376-0.1098-0.1180.1118-0.0644-0.19550.0950.39930.84760.29050.75940.32240.15311.01620.20850.8187.1653-17.5696-24.5964
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1:68 OR RESID 118:151)A1 - 68
2X-RAY DIFFRACTION1CHAIN A AND (RESID 1:68 OR RESID 118:151)A118 - 151
3X-RAY DIFFRACTION2CHAIN A AND (RESID 69:117)A69 - 117
4X-RAY DIFFRACTION3CHAIN BB1 - 6

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