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- PDB-4hgu: Crystal Structure of Galleria mellonella Silk Protease Inhibitor 2 -

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Basic information

Entry
Database: PDB / ID: 4hgu
TitleCrystal Structure of Galleria mellonella Silk Protease Inhibitor 2
ComponentsSilk protease inhibitor 2
KeywordsHYDROLASE INHIBITOR / KAZAL-TYPE SERINE PROTEASE INHIBITOR
Function / homology
Function and homology information


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
Silk protease inhibitor 2
Similarity search - Component
Biological speciesGalleria mellonella (greater wax moth)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.98 Å
AuthorsKrzywda, S. / Jaskolski, M. / Dvornyk, A. / Kludkiewicz, B. / Grzelak, K. / Zagorski, W. / Bal, W. / Kopera, E.
CitationJournal: Plos One / Year: 2014
Title: Atomic resolution structure of a protein prepared by non-enzymatic His-tag removal. Crystallographic and NMR study of GmSPI-2 inhibitor.
Authors: Kopera, E. / Bal, W. / Lenarcic Zivkovic, M. / Dvornyk, A. / Kludkiewicz, B. / Grzelak, K. / Zhukov, I. / Zagorski-Ostoja, W. / Jaskolski, M. / Krzywda, S.
History
DepositionOct 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Sep 20, 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_alt_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_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_alt_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_ptnr2_label_alt_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_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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Silk protease inhibitor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,4105
Polymers4,3181
Non-polymers924
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.27, 31.24, 35.74
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide Silk protease inhibitor 2


Mass: 4317.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Galleria mellonella (greater wax moth) / Plasmid: pPICZalphaB / Production host: Pichia pastoris (fungus) / References: UniProt: Q968S7
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 1.76 Å3/Da / Density % sol: 30.23 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.4 M sodium citrate and 0.1 M Hepes pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.80000,0.91841
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 5, 2009 / Details: mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.81
20.918411
ReflectionResolution: 0.98→20 Å / Num. all: 17179 / Num. obs: 17179 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.9 % / Biso Wilson estimate: 2.04 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 22.52
Reflection shellResolution: 0.98→1.01 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.04 / Num. unique all: 1105 / % possible all: 84.5

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Processing

Software
NameClassification
MxCuBEdata collection
MOLREPphasing
SHELXL-97refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AN1

1an1


Resolution: 0.98→20 Å / Num. parameters: 3821 / Num. restraintsaints: 3967 / Isotropic thermal model: ANISOTROPIC / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: ANISOTROPIC REFINEMENT. CONJUGATE GRADIENT LEAST SQUARES REFINEMENT WITH RESTRAINTS APPLIED ONLY TO RESIDUES IN DOUBLE CONFORMATION. HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1236 1031 6 %RANDOM
Rwork0.106 ---
obs0.1057 17179 94.8 %-
all-17179 --
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 17 / Occupancy sum hydrogen: 260.62 / Occupancy sum non hydrogen: 356.69
Refinement stepCycle: LAST / Resolution: 0.98→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms300 0 4 81 385
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.023
X-RAY DIFFRACTIONs_angle_d0.058
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0637
X-RAY DIFFRACTIONs_zero_chiral_vol0.142
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.114
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.022
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.007
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.039
X-RAY DIFFRACTIONs_approx_iso_adps0.053

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