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- PDB-1ga1: CRYSTAL STRUCTURE ANALYSIS OF PSCP (PSEUDOMONAS SERINE-CARBOXYL P... -

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Basic information

Entry
Database: PDB / ID: 1ga1
TitleCRYSTAL STRUCTURE ANALYSIS OF PSCP (PSEUDOMONAS SERINE-CARBOXYL PROTEINASE) COMPLEXED WITH A FRAGMENT OF IODOTYROSTATIN (THIS ENZYME RENAMED "SEDOLISIN" IN 2003)
Components
  • FRAGMENT OF IODOTYROSTATIN
  • SERINE-CARBOXYL PROTEINASE
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SERINE-CARBOXYL PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


sedolisin / tripeptidyl-peptidase activity / periplasmic space / serine-type endopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Peptidase S53, activation domain / Sedolisin domain / : / Pro-kumamolisin, activation domain / Sedolisin domain profile. / Pro-kumamolisin, activation domain / Peptidase S8/S53 domain / Peptidase S8, subtilisin, Ser-active site / Peptidase S8/S53 domain superfamily / Subtilase family ...Peptidase S53, activation domain / Sedolisin domain / : / Pro-kumamolisin, activation domain / Sedolisin domain profile. / Pro-kumamolisin, activation domain / Peptidase S8/S53 domain / Peptidase S8, subtilisin, Ser-active site / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SINGLE-WAVELENGTH ANOMALOUS DIFFRACTION / Resolution: 1.4 Å
AuthorsDauter, Z. / Li, M. / Wlodawer, A.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Practical experience with the use of halides for phasing macromolecular structures: a powerful tool for structural genomics.
Authors: Dauter, Z. / Li, M. / Wlodawer, A.
#1: Journal: Nat.Struct.Biol. / Year: 2001
Title: Carboxyl Proteinase from Pseudomonas Defines a Novel Family of Subtilisin-like Enzymes
Authors: Wlodawer, A. / Li, M. / Dauter, Z. / Gustchina, A. / Uchida, K. / Oyama, H. / Dunn, B.M. / Oda, K.
History
DepositionNov 29, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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_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.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 / _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: SERINE-CARBOXYL PROTEINASE
I: FRAGMENT OF IODOTYROSTATIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0755
Polymers38,9072
Non-polymers1683
Water7,602422
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.190, 97.190, 83.370
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11A-472-

HOH

21A-596-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AI

#1: Protein SERINE-CARBOXYL PROTEINASE / PSCP / PSEUDOMONAPEPSIN / PEPSTATIN-INSENSITIVE CARBOXYL PROTEINASE


Mass: 38446.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Plasmid: PUKCP2212 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P42790, EC: 3.4.23.37
#2: Protein/peptide FRAGMENT OF IODOTYROSTATIN


Mass: 461.296 Da / Num. of mol.: 1 / Mutation: T2(PHI) / Source method: obtained synthetically / Details: The inhibitor was chemically synthesized.

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Non-polymers , 4 types, 425 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTYROSTATIN IS A NATURAL INHIBITOR, COMPOSED OF ISOVALERYL-TYROSYL-LEUSYL-TYROSINAL. IN 1GA1 AND ...TYROSTATIN IS A NATURAL INHIBITOR, COMPOSED OF ISOVALERYL-TYROSYL-LEUSYL-TYROSINAL. IN 1GA1 AND 1GA4, THE PROTEIN WAS CRYSTALLIZED WITH THE VARIANT OF THIS INHIBITOR, WHERE THE SECOND TYR HAD IODINE INSTEAD OF HYDROXYL, SO IN FACT IT IS P-IODOPHENYLALANINE. IN 1GA6, TYR WAS USED. WHAT THE AUTHORS OBSERVED IN 1GA4, WAS THE TRIPEPTIDE NOT TETRAPEPTIDE, LACKING THE LEU RESIDUE BETWEEN TWO AROMATIC RESIDUES. THIS IS CERTAIN, BUT IT IS NOT CLEAR HOW SUCH A MODIFIED ENTITY ENDED UP IN THE STRUCTURE, AS DISCUSSED IN REFERENCE 1. IN 1GA1 AND 1GA6 ONLY PARTS OF THE INHIBITOR (PARTIALLY OCCUPIED AS WELL) ARE VISIBLE IN THE ELECTRON DENSITY AND ARE MODELED AS A TYROSINE IN 1GA6 AND IODOPHENYLALANINE IN 1GA1 ACCOMPANIED BY JUST MAIN CHAIN PARTS OF ADJOINING RESIDUES, THEREFORE REPRESENTED AS UNK, UNKNOWNS. IN 1GA6 THERE WAS NO DENSITY FOR THE RESIDUE EXPECTED TO BIND TO THE N-TERMINUS OF THE AROMATIC. THE IDENTIFICATION OF IODINE IN 1GA1 WAS CONFIRMED UNEQUIVOCALLY BY ITS ANOMALOUS SCATTERING SIGNAL IN THE ANOMALOUS FOURIER MAP. THEREFORE IN 1GA4 THE AUTHORS CALLED THE MODIFIED INHIBITOR, LACKING LEU IN THE MIDDLE, AS "PSEUDOIODOTYROSTATIN". IN TWO OTHER STRUCTURES THE AUTHORS ARE NOT SURE WHAT IS REALLY THERE, SO THE INHIBITOR IS DESCRIBED AS "FRAGMENTS OF IODOTYROSTATIN" IN 1GA1 AND "FRAGMENTS OF TYROSTATIN" IN 1GA6.
Has protein modificationY

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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: 2.92 Å3/Da / Density % sol: 57.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M sodium chloride, 5 mM calcium chloride, 1.4 M lithium sulfate, 0.1 M Tris buffer pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 4.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
20.1 M1dropNaCl
35 mM1dropCaCl2
450 mMsodium acetate1drop
51.4 Mlithium sulfate1reservoir
60.1 MTris1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 3, 2000 / Details: focussing mirror
RadiationMonochromator: Si(111) double crystal, sagitally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. all: 87947 / Num. obs: 87947 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 50.2
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 7 / Num. unique all: 8711 / % possible all: 99.5
Reflection
*PLUS
Num. measured all: 677827
Reflection shell
*PLUS
% possible obs: 99.5 %

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Processing

Software
NameClassification
HKL-2000data collection
HKL-2000data reduction
SHELXDphasing
SHARPphasing
DMmodel building
WARPmodel building
SHELXL-97refinement
HKL-2000data scaling
DMphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SINGLE-WAVELENGTH ANOMALOUS DIFFRACTION
Resolution: 1.4→30 Å / σ(F): -999 / σ(I): -999 / Stereochemistry target values: Engh & Huber
Details: Anisotropic refinement of individual atoms. Parameter errors estimated from least-squares blocked full-matrix inversion.
RfactorNum. reflectionSelection details
Rfree0.1358 8107 RANDOM
Rwork0.113 --
all0.1129 87947 -
obs0.108 81364 -
Refinement stepCycle: LAST / Resolution: 1.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2726 0 8 422 3156
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_from_restr_planes0.028
X-RAY DIFFRACTIONs_zero_chiral_vol0.079
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.089
LS refinement shellResolution: 1.4→30 Å
RfactorNum. reflection% reflection
Rfree0.1358 8801 -
Rwork0.1129 --
obs-87947 93 %
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 0.1129 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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