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- PDB-4gaw: Crystal structure of active human granzyme H -

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Basic information

Entry
Database: PDB / ID: 4gaw
TitleCrystal structure of active human granzyme H
ComponentsGranzyme HGranzyme B
KeywordsHYDROLASE / serine protease / Cytolysis / cytotoxic granules
Function / homology
Function and homology information


cytolytic granule / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / Metabolism of Angiotensinogen to Angiotensins / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / killing of cells of another organism / serine-type endopeptidase activity / intracellular membrane-bounded organelle / apoptotic process / proteolysis / membrane / cytoplasm
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Granzyme H
B: Granzyme H
C: Granzyme H
D: Granzyme H
E: Granzyme H
F: Granzyme H
G: Granzyme H
H: Granzyme H
I: Granzyme H
J: Granzyme H
K: Granzyme H
L: Granzyme H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)304,09630
Polymers302,54912
Non-polymers1,54718
Water68538
1
A: Granzyme H


Theoretical massNumber of molelcules
Total (without water)25,2121
Polymers25,2121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Granzyme H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5975
Polymers25,2121
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Granzyme H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2482
Polymers25,2121
Non-polymers351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Granzyme H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5365
Polymers25,2121
Non-polymers3244
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Granzyme H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3082
Polymers25,2121
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Granzyme H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5014
Polymers25,2121
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Granzyme H


Theoretical massNumber of molelcules
Total (without water)25,2121
Polymers25,2121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Granzyme H


Theoretical massNumber of molelcules
Total (without water)25,2121
Polymers25,2121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: Granzyme H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4404
Polymers25,2121
Non-polymers2283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
J: Granzyme H


Theoretical massNumber of molelcules
Total (without water)25,2121
Polymers25,2121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
11
K: Granzyme H


Theoretical massNumber of molelcules
Total (without water)25,2121
Polymers25,2121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
12
L: Granzyme H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4053
Polymers25,2121
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)170.369, 367.070, 61.137
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Granzyme H / Granzyme B / CCP-X / Cathepsin G-like 2 / CTSGL2 / Cytotoxic T-lymphocyte proteinase / Cytotoxic serine protease C / CSP-C


Mass: 25212.416 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GZMH, CGL2, CTSGL2 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta(DE3)
References: UniProt: P20718, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 3.16 Å3/Da / Density % sol: 61.07 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M Li2SO4, 0.1M Bicine (pH8.5), 25% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 7, 2009
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, direct water cooling using micro-channel (1st crystal), indirect water cooling (2nd crystal)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3→39.8 Å / Num. all: 78537 / Num. obs: 78537 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 19.7
Reflection shellResolution: 3→3.11 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 6.3 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
COMOphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TK9

3tk9


Resolution: 3→39.8 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.854 / SU B: 54.981 / SU ML: 0.436 / Cross valid method: THROUGHOUT / ESU R Free: 0.5 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT 2. THE ELECTRON DENSITY MAP FOR CHAIN L IS VERY WEAK
RfactorNum. reflection% reflectionSelection details
Rfree0.30593 3931 5 %RANDOM
Rwork0.27069 ---
obs0.27249 74302 99.8 %-
all-74438 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.066 Å2
Baniso -1Baniso -2Baniso -3
1--1.61 Å20 Å2-0 Å2
2--0.23 Å2-0 Å2
3---1.38 Å2
Refinement stepCycle: LAST / Resolution: 3→39.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21176 0 78 38 21292
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01921759
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8671.96829410
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.55452690
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.11123.063862
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.053153939
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.39115156
X-RAY DIFFRACTIONr_chiral_restr0.1170.23225
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02116087
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: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.448 267 -
Rwork0.389 5001 -
obs--99.79 %
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)
12.00041.0622-0.91671.2955-1.07890.9649-0.23890.4227-0.3298-0.0983-0.0129-0.0836-0.04090.03080.25190.5499-0.1005-0.0280.27980.05970.8142-64.126786.3975-17.8954
23.0467-0.57590.90193.4775-0.88632.5483-0.1714-0.06380.2176-0.10690.0603-0.15570.0128-0.05090.11110.37650.0091-0.03290.32430.1270.216429.413960.608715.8664
31.2211-0.77420.10832.70321.45391.1881-0.3262-0.28410.2749-0.08230.0062-0.0827-0.1086-0.23970.320.42330.0846-0.06890.6525-0.23550.6823-56.208530.968815.7626
40.8912-0.15590.0132.13471.23642.3059-0.36780.00040.22760.06160.37090.39550.05690.5972-0.00310.36910.0836-0.05850.85110.07330.219956.587761.4436-13.882
51.34921.25020.58342.43661.16940.7747-0.5515-0.3948-0.0702-0.39390.46890.3236-0.10150.22840.08250.52010.1777-0.05820.87080.13170.326764.49426.030313.5111
61.9549-0.83680.73444.6464-1.061.6132-0.225-0.0131-0.00390.5050.360.1162-0.1718-0.1392-0.1350.40260.0339-0.030.28110.10820.341221.27835.116-10.3616
72.37321.8816-0.97942.6088-1.3871.4622-0.3250.2149-0.046-0.34480.3970.2921-0.0301-0.0626-0.0720.4644-0.0843-0.19450.410.2710.464811.33430.233425.8291
81.0083-1.212-0.92482.25411.52211.1446-0.5092-0.30420.15710.27190.782-0.11450.23650.4679-0.27280.58540.4541-0.15871.3166-0.20910.323974.813531.7135-23.6996
92.24370.50750.02792.8573-1.77131.9285-0.18330.36150.53270.084-0.0422-0.10770.0694-0.31070.22550.3736-0.0137-0.16450.30380.08310.6416-28.930530.065-15.8931
101.29761.05680.88341.26211.05931.1316-0.5940.03350.3363-0.2880.16570.6852-0.16840.41890.42830.60740.0557-0.44650.35360.18621.2703-10.132959.9744-5.2997
112.2753-2.40271.25072.6121-1.37041.4159-1.0601-0.50051.26420.95010.4805-1.4762-0.1929-1.21380.57950.677-0.0637-0.71871.444-0.54071.2645-74.027261.51376.2677
125.6178-1.6796-0.855.20952.04062.531-0.2446-0.5654-0.14990.2491-0.1551.6503-0.293-0.25440.39971.00020.1098-0.13460.41550.06261.78-20.764285.619617.7302
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 304
2X-RAY DIFFRACTION2B16 - 403
3X-RAY DIFFRACTION3C16 - 301
4X-RAY DIFFRACTION4D16 - 406
5X-RAY DIFFRACTION5E16 - 404
6X-RAY DIFFRACTION6F16 - 404
7X-RAY DIFFRACTION7G16 - 301
8X-RAY DIFFRACTION8H16 - 301
9X-RAY DIFFRACTION9I16 - 408
10X-RAY DIFFRACTION10J16 - 301
11X-RAY DIFFRACTION11K16 - 302
12X-RAY DIFFRACTION12L16 - 404

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