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- PDB-4ga7: Crystal structure of human serpinB1 mutant -

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Basic information

Entry
Database: PDB / ID: 4ga7
TitleCrystal structure of human serpinB1 mutant
ComponentsLeukocyte elastase inhibitor
KeywordsHYDROLASE INHIBITOR / serpin / Conformational change / serine protease inhibitor / Cathepsin G inhibitor / chymase inhibitor / chymotrypsin inhibitor
Function / homology
Function and homology information


cytolytic granule / negative regulation of endopeptidase activity / peptidase inhibitor activity / type B pancreatic cell proliferation / negative regulation of interleukin-1 beta production / negative regulation of cell migration / serine-type endopeptidase inhibitor activity / cytoplasmic ribonucleoprotein granule / : / secretory granule lumen ...cytolytic granule / negative regulation of endopeptidase activity / peptidase inhibitor activity / type B pancreatic cell proliferation / negative regulation of interleukin-1 beta production / negative regulation of cell migration / serine-type endopeptidase inhibitor activity / cytoplasmic ribonucleoprotein granule / : / secretory granule lumen / early endosome / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / membrane
Similarity search - Function
Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily ...Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / 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
Leukocyte elastase inhibitor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsWang, L. / Li, Q. / Wu, L. / Zhang, K. / Tong, L. / Sun, F. / Fan, Z.
CitationJournal: J.Immunol. / Year: 2013
Title: Identification of SERPINB1 as a physiological inhibitor of human granzyme H
Authors: Wang, L. / Li, Q. / Wu, L. / Liu, S. / Zhang, Y. / Yang, X. / Zhu, P. / Zhang, H. / Zhang, K. / Lou, J. / Liu, P. / Tong, L. / Sun, F. / Fan, Z.
History
DepositionJul 25, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Nov 8, 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 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leukocyte elastase inhibitor
B: Leukocyte elastase inhibitor


Theoretical massNumber of molelcules
Total (without water)87,8782
Polymers87,8782
Non-polymers00
Water30617
1
A: Leukocyte elastase inhibitor


Theoretical massNumber of molelcules
Total (without water)43,9391
Polymers43,9391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Leukocyte elastase inhibitor


Theoretical massNumber of molelcules
Total (without water)43,9391
Polymers43,9391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.339, 67.339, 180.288
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Leukocyte elastase inhibitor / LEI / Monocyte/neutrophil elastase inhibitor / EI / M/NEI / Peptidase inhibitor 2 / PI-2 / Serpin B1


Mass: 43938.754 Da / Num. of mol.: 2 / Mutation: L346D,M347D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINB1, ELANH2, MNEI, PI2 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta(DE3) / References: UniProt: P30740
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.11 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.18M Lithium citrate tribasic tetrahydrate, 18% w/v Polyethylene glycol 3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 14, 2011
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 17868 / Num. obs: 17850 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.1 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 35
Reflection shellResolution: 2.9→3 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 7 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BY7

1by7


Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.928 / SU B: 31.687 / SU ML: 0.267 / Cross valid method: THROUGHOUT / ESU R Free: 0.406 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23202 905 5.1 %RANDOM
Rwork0.18315 ---
obs0.18554 16846 99.84 %-
all-16918 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.794 Å2
Baniso -1Baniso -2Baniso -3
1-2.32 Å20 Å20 Å2
2--2.32 Å20 Å2
3----4.64 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5893 0 0 17 5910
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.026014
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1241.968105
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6045732
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.61524.792288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.707151097
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2581528
X-RAY DIFFRACTIONr_chiral_restr0.0760.2892
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214518
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 56 -
Rwork0.284 1216 -
obs--99.84 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6267-0.28670.39910.5967-0.070.9645-0.0279-0.07780.05070.121-0.02240.0417-0.0906-0.05370.05030.067-0.01970.02790.0483-0.0330.028838.23338.0413-6.7098
20.6776-0.05030.4790.2720.00561.0620.02520.1026-0.0667-0.0002-0.02520.06910.19590.1684-00.05340.02740.00690.0552-0.03530.0507-19.241351.3235-30.8451
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 405
2X-RAY DIFFRACTION2B1 - 412

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