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- PDB-1xqg: 3.10 A crystal structure of maspin, Space group P 4 21 2 -

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Basic information

Entry
Database: PDB / ID: 1xqg
Title3.10 A crystal structure of maspin, Space group P 4 21 2
ComponentsMaspin
KeywordsANTITUMOR PROTEIN / SERPIN / MASPIN / TUMOR SUPPRESSION
Function / homology
Function and homology information


prostate gland morphogenesis / cornified envelope / regulation of epithelial cell proliferation / sarcoplasm / extracellular matrix organization / morphogenesis of an epithelium / serine-type endopeptidase inhibitor activity / extracellular space / cytoplasm
Similarity search - Function
Maspin, serpin domain / Serpin B9/maspin / 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 ...Maspin, serpin domain / Serpin B9/maspin / 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: 3.1 Å
AuthorsAl-Ayyoubi, M. / Gettins, P.G. / Volz, K.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal Structure of Human Maspin, a Serpin with Antitumor Properties: Reactive Center Loop of Mapsin is Exposed but Constrained
Authors: Al-Ayyoubi, M. / Gettins, P.G. / Volz, K.
History
DepositionOct 12, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 600HETEROGEN HOH 1-76 ARE ASSOCIATED WITH CHAIN A. HOH 101-177 ARE ASSOCIATED WITH CHAIN B.
Remark 999SEQUENCE THE AUTHORS STATE THAT RESIDUES 66, 176, AND 187 WERE VAL, SER, AND VAL IN THE CONSTRUCT, ...SEQUENCE THE AUTHORS STATE THAT RESIDUES 66, 176, AND 187 WERE VAL, SER, AND VAL IN THE CONSTRUCT, WHICH CONFLICTS WITH SWS ENTRY P36952.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maspin
B: Maspin


Theoretical massNumber of molelcules
Total (without water)87,5512
Polymers87,5512
Non-polymers00
Water2,738152
1
A: Maspin


Theoretical massNumber of molelcules
Total (without water)43,7761
Polymers43,7761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Maspin


Theoretical massNumber of molelcules
Total (without water)43,7761
Polymers43,7761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)147.462, 147.462, 118.038
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein Maspin /


Mass: 43775.551 Da / Num. of mol.: 2
Mutation: C20S, C34A, C183S, C205S, C214S, C287S, C323S, C373S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINB5, PI5 / Plasmid: PQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: P36952
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 3.9 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 45% PEG400, SODIUM CITRATE 0.2M, TRIS 0.1M, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 10, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 23502 / % possible obs: 97.5 % / Redundancy: 4.9 % / Biso Wilson estimate: 42.1 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.4
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.1 / % possible all: 95.6

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Processing

Software
NameClassification
HKL-2000data collection
HKL-2000data reduction
CNSrefinement
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB IDS 1HLE, 1BY7, 1OVA

1hle

1by7

1ova


Resolution: 3.1→43.98 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 200322.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.252 241 1 %RANDOM
Rwork0.194 ---
obs0.194 23042 95.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 20.4195 Å2 / ksol: 0.338206 e/Å3
Displacement parametersBiso mean: 40.9 Å2
Baniso -1Baniso -2Baniso -3
1-5.16 Å20 Å20 Å2
2--5.16 Å20 Å2
3----10.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 3.1→43.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5922 0 0 152 6074
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.289 35 1 %
Rwork0.269 3415 -
obs--87.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMCARBOHYDRATE.PARAM
X-RAY DIFFRACTION3CARBOHYDRATE.PARAMWATER.PARAM

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