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- PDB-1mtp: The X-ray crystal structure of a serpin from a thermophilic prokaryote -

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Basic information

Entry
Database: PDB / ID: 1mtp
TitleThe X-ray crystal structure of a serpin from a thermophilic prokaryote
Components
  • Serine Proteinase Inhibitor (SERPIN), Chain A
  • Serine Proteinase Inhibitor (SERPIN), Chain B
KeywordsSTRUCTURAL GENOMICS / protease inhibitor
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / extracellular space
Similarity search - Function
Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) ...Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Proteinase inhibitor I4, serpin
Similarity search - Component
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsIrving, J.A. / Cabrita, L.D. / Rossjohn, J. / Pike, R.N. / Bottomley, S.P. / Whisstock, J.C.
CitationJournal: Structure / Year: 2003
Title: The 1.5 A crystal structure of a prokaryote serpin: controlling conformational change in a heated environment
Authors: Irving, J.A. / Cabrita, L.D. / Rossjohn, J. / Pike, R.N. / Bottomley, S.P. / Whisstock, J.C.
History
DepositionSep 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine Proteinase Inhibitor (SERPIN), Chain A
B: Serine Proteinase Inhibitor (SERPIN), Chain B


Theoretical massNumber of molelcules
Total (without water)39,7642
Polymers39,7642
Non-polymers00
Water10,881604
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-27 kcal/mol
Surface area13870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.936, 65.595, 124.737
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Serine Proteinase Inhibitor (SERPIN), Chain A


Mass: 34976.918 Da / Num. of mol.: 1 / Fragment: Chain A, residue 55-377
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca (bacteria) / Production host: Escherichia coli (E. coli) / References: GenBank: 23019748, UniProt: Q47NK3*PLUS
#2: Protein/peptide Serine Proteinase Inhibitor (SERPIN), Chain B


Mass: 4787.580 Da / Num. of mol.: 1 / Fragment: Chain B, residue 378-420
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca (bacteria) / Production host: Escherichia coli (E. coli) / References: GenBank: 23019748, UniProt: Q47NK3*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 604 / 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: 2.16 Å3/Da / Density % sol: 42.94 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG 4000, 0.1 M Tris, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
PH range low: 9 / PH range high: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
220-30 %PEG40001reservoir
30.1 MTris-HCl1reservoirpH8-9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 14, 2002 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 179258 / Num. obs: 179258 / Observed criterion σ(I): 0
Reflection
*PLUS
Num. obs: 54979 / % possible obs: 98.1 % / Redundancy: 3.3 % / Num. measured all: 179258 / Rmerge(I) obs: 0.043
Reflection shell
*PLUS
% possible obs: 92 % / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 2.6

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Processing

Software
NameClassification
ARP/wARPmodel building
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HLE

1hle


Resolution: 1.5→50 Å
RfactorNum. reflection
Rfree0.223 -
Rwork0.195 -
all-179258
obs-179258
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2714 0 0 604 3318
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 3 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.004
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.33
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.41
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.88

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