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- PDB-4gi3: Crystal structure of Greglin in complex with subtilisin -

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Basic information

Entry
Database: PDB / ID: 4gi3
TitleCrystal structure of Greglin in complex with subtilisin
Components
  • Greglin
  • KerA
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Kazal type inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Subtilisin Carlsberg-like catalytic domain / Kazal domain superfamily / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site ...Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Subtilisin Carlsberg-like catalytic domain / Kazal domain superfamily / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus licheniformis (bacteria)
Schistocerca gregaria (desert locust)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsKellenberger, C. / Roussel, A.
CitationJournal: Febs J. / Year: 2012
Title: Crystal structure of greglin, a novel non-classical Kazal inhibitor, in complex with subtilisin
Authors: Derache, C. / Epinette, C. / Roussel, A. / Gabant, G. / Cadene, M. / Korkmaz, B. / Gauthier, F. / Kellenberger, C.
History
DepositionAug 8, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Nov 8, 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 / 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

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Assembly

Deposited unit
A: KerA
C: Greglin


Theoretical massNumber of molelcules
Total (without water)36,6382
Polymers36,6382
Non-polymers00
Water6,630368
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-12 kcal/mol
Surface area12370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.070, 39.708, 59.750
Angle α, β, γ (deg.)90.00, 98.05, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein KerA


Mass: 27437.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus licheniformis (bacteria) / References: UniProt: Q9FDF2
#2: Protein Greglin


Mass: 9200.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schistocerca gregaria (desert locust) / Cell: ovaries / References: UniProt: P85064
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE DEPOSITORS STATE THAT RESIDUES ALA7, THR17, CYS21, CYS25, GLN39 IN THE CHAIN C ARE CORRECT AND ...THE DEPOSITORS STATE THAT RESIDUES ALA7, THR17, CYS21, CYS25, GLN39 IN THE CHAIN C ARE CORRECT AND THAT THE PREVIOUSLY DEPOSITED SEQUENCE IN SWISSPROT WAS INCORRECT AT THESE POSITIONS

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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: 2.1 Å3/Da / Density % sol: 41.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.68M sodium citrate, 0.36M sodium formate, 0.066M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 23, 2011 / Details: mirrors
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.75→32.57 Å / Num. all: 31070 / Num. obs: 31070 / % possible obs: 100 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Biso Wilson estimate: 19.53 Å2 / Rsym value: 0.078
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.462 / % possible all: 100

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Processing

Software
NameVersionClassification
DNAdata collection
AMoREphasing
BUSTER2.11.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YU6

1yu6


Resolution: 1.75→32.57 Å / Cor.coef. Fo:Fc: 0.9473 / Cor.coef. Fo:Fc free: 0.9332 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.115 / SU Rfree Blow DPI: 0.108 / SU Rfree Cruickshank DPI: 0.104
RfactorNum. reflection% reflectionSelection details
Rfree0.2007 1582 5.09 %RANDOM
Rwork0.166 ---
obs0.1679 31066 100 %-
Displacement parametersBiso max: 105.14 Å2 / Biso mean: 23.2177 Å2 / Biso min: 5.73 Å2
Baniso -1Baniso -2Baniso -3
1-2.5854 Å20 Å22.6994 Å2
2--3.7886 Å20 Å2
3----6.3741 Å2
Refine analyzeLuzzati coordinate error obs: 0.183 Å
Refinement stepCycle: LAST / Resolution: 1.75→32.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2361 0 0 368 2729
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d763SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes51HARMONIC2
X-RAY DIFFRACTIONt_gen_planes365HARMONIC5
X-RAY DIFFRACTIONt_it2408HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion328SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3177SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2408HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3287HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion3.26
X-RAY DIFFRACTIONt_other_torsion14.96
LS refinement shellResolution: 1.75→1.81 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2783 151 5.3 %
Rwork0.2157 2698 -
all0.2191 2849 -
obs--100 %

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