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- PDB-2zv6: Crystal structure of human squamous cell carcinoma antigen 1 -

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Basic information

Entry
Database: PDB / ID: 2zv6
TitleCrystal structure of human squamous cell carcinoma antigen 1
ComponentsSerpin B3
KeywordsHYDROLASE INHIBITOR / serine proteinase inhibitor / reactive site loop / Acetylation / Alternative splicing / Cytoplasm / Polymorphism / Protease inhibitor / Serine protease inhibitor
Function / homology
Function and homology information


negative regulation of peptidase activity / autocrine signaling / positive regulation of endopeptidase activity / negative regulation of catalytic activity / negative regulation of JUN kinase activity / negative regulation of endopeptidase activity / paracrine signaling / cysteine-type endopeptidase inhibitor activity / positive regulation of epithelial to mesenchymal transition / negative regulation of proteolysis ...negative regulation of peptidase activity / autocrine signaling / positive regulation of endopeptidase activity / negative regulation of catalytic activity / negative regulation of JUN kinase activity / negative regulation of endopeptidase activity / paracrine signaling / cysteine-type endopeptidase inhibitor activity / positive regulation of epithelial to mesenchymal transition / negative regulation of proteolysis / serine-type endopeptidase inhibitor activity / azurophil granule lumen / virus receptor activity / cytoplasmic vesicle / protease binding / vesicle / positive regulation of cell migration / positive regulation of cell population proliferation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / nucleus / plasma membrane / cytosol / cytoplasm
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsZheng, B. / Matoba, Y. / Katagiri, C. / Hibino, T. / Sugiyama, M.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: Crystal structure of SCCA1 and insight about the interaction with JNK1
Authors: Zheng, B. / Matoba, Y. / Kumagai, T. / Katagiri, C. / Hibino, T. / Sugiyama, M.
History
DepositionNov 1, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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: Serpin B3
B: Serpin B3
C: Serpin B3


Theoretical massNumber of molelcules
Total (without water)137,6843
Polymers137,6843
Non-polymers00
Water5,621312
1
A: Serpin B3


Theoretical massNumber of molelcules
Total (without water)45,8951
Polymers45,8951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serpin B3


Theoretical massNumber of molelcules
Total (without water)45,8951
Polymers45,8951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Serpin B3


Theoretical massNumber of molelcules
Total (without water)45,8951
Polymers45,8951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)263.480, 263.480, 48.670
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-393-

HOH

21B-416-

HOH

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Components

#1: Protein Serpin B3 / Squamous cell carcinoma antigen 1 / SCCA-1 / Protein T4-A


Mass: 45894.785 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINB3, SCCA, SCCA1 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29508
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.36 Å3/Da / Density % sol: 47.91 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.3M sodium citrate, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 21, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 31292 / Num. obs: 31292 / % possible obs: 90.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 59.7 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 20.7
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 2 / Num. unique all: 3181 / Rsym value: 0.476 / % possible all: 93.2

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 1OVA

1ova


Resolution: 2.7→30 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
Details: BULK SOLVENT MODEL WAS USED. NCS restrain was imposed.
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1300 4.9 %RANDOM
Rwork0.19 ---
obs0.19 26363 76.3 %-
all-26363 --
Displacement parametersBiso mean: 65.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.73 Å0.6 Å
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8729 0 0 312 9041
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.59
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it5.071.5
X-RAY DIFFRACTIONx_mcangle_it7.892
X-RAY DIFFRACTIONx_scbond_it7.352
X-RAY DIFFRACTIONx_scangle_it10.312.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.376 151 4.6 %
Rwork0.341 3162 -
obs--57.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramtophcsdx.proam
X-RAY DIFFRACTION2toph19.sol

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