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- PDB-2erw: Crystal Structure of Infestin 4, a factor XIIa inhibitor -

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Basic information

Entry
Database: PDB / ID: 2erw
TitleCrystal Structure of Infestin 4, a factor XIIa inhibitor
Componentsserine protease inhibitor infestin
KeywordsBLOOD CLOTTING / HYDROLASE INHIBITOR / Kazal type domain
Function / homology
Function and homology information


Kazal-type serine protease inhibitor domain / Kazal serine protease inhibitors family signature. / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Thrombin inhibitor infestin
Similarity search - Component
Biological speciesTriatoma infestans (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsCampos, I.T.N. / Tanaka, A.S. / Barbosa, J.A.R.G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: The Kazal-type inhibitors infestins 1 and 4 differ in specificity but are similar in three-dimensional structure.
Authors: Campos, I.T. / Souza, T.A. / Torquato, R.J. / De Marco, R. / Tanaka-Azevedo, A.M. / Tanaka, A.S. / Barbosa, J.A.R.G.
History
DepositionOct 25, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jun 20, 2012Group: Database references
Revision 1.4Jul 5, 2017Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Aug 23, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: serine protease inhibitor infestin


Theoretical massNumber of molelcules
Total (without water)6,1981
Polymers6,1981
Non-polymers00
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.765, 45.377, 56.771
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAsymmetric unit content is the biological assembly.

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Components

#1: Protein serine protease inhibitor infestin


Mass: 6198.125 Da / Num. of mol.: 1 / Fragment: residues 167-222
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triatoma infestans (insect) / Plasmid: pPIC9 / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: Q95P16
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.68 Å3/Da / Density % sol: 54.03 %
Crystal growTemperature: 303 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 30% PEG 4000, 0.1 M ammonium acetate, 0.1 M sodium cacodylate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.427 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 9, 2004
RadiationMonochromator: Si CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.427 Å / Relative weight: 1
ReflectionResolution: 1.4→40 Å / Num. all: 13756 / Num. obs: 13618 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 15.315 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 52.5
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 5.7 / Num. unique all: 1229 / % possible all: 91

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TBR

1tbr


Resolution: 1.4→35.71 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.712 / SU ML: 0.034 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: SIMULATED ANNEALING WAS PERFORMED WITH THE CNS SOFTWARE IN THE FIRST CYCLE OF REFINEMENT. TLS APPLIED USING THE PROTEIN MODEL AS ONE GROUP. Close contacts in remark 500 are related to the ...Details: SIMULATED ANNEALING WAS PERFORMED WITH THE CNS SOFTWARE IN THE FIRST CYCLE OF REFINEMENT. TLS APPLIED USING THE PROTEIN MODEL AS ONE GROUP. Close contacts in remark 500 are related to the alternate conformations of the CYS 6 region close to the N-terminus and CYS 31. The alternate conformation of the N-terminus is not modelled due to the weak electron density.
RfactorNum. reflection% reflectionSelection details
Rfree0.1895 676 5 %RANDOM
Rwork0.18014 ---
all0.1806 13610 --
obs0.1806 13574 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.051 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.21 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.4→35.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms402 0 0 74 476
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022432
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.968582
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.936552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.22423.8121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4541579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.321154
X-RAY DIFFRACTIONr_chiral_restr0.0830.259
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02332
X-RAY DIFFRACTIONr_nbd_refined0.2440.2212
X-RAY DIFFRACTIONr_nbtor_refined0.3220.2308
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.291
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.28
X-RAY DIFFRACTIONr_mcbond_it0.741.5269
X-RAY DIFFRACTIONr_mcangle_it1.2192430
X-RAY DIFFRACTIONr_scbond_it1.7643178
X-RAY DIFFRACTIONr_scangle_it2.9544.5152
LS refinement shellResolution: 1.403→1.439 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 55 -
Rwork0.329 904 -
obs-904 97.96 %
Refinement TLS params.Method: refined / Origin x: 12.833 Å / Origin y: 7.551 Å / Origin z: 24.913 Å
111213212223313233
T-0.1661 Å20.0011 Å20.0157 Å2--0.1594 Å2-0.0078 Å2---0.1346 Å2
L3.33 °20.357 °20.3214 °2-3.8251 °20.189 °2--1.6965 °2
S-0.0121 Å °0.0534 Å °-0.1421 Å °-0.1988 Å °0.0332 Å °-0.1068 Å °0.1021 Å °0.0824 Å °-0.0211 Å °

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