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- PDB-1xu8: The 2.8 A structure of a tumour suppressing serpin -

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Basic information

Entry
Database: PDB / ID: 1xu8
TitleThe 2.8 A structure of a tumour suppressing serpin
ComponentsMaspin
KeywordsSIGNALING PROTEIN / maspin / serpin / tumor suppressor / SERPINB5
Function / homology
Function and homology information


prostate gland morphogenesis / regulation of epithelial cell proliferation / cornified envelope / 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 / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsIrving, J.A. / Law, R.H. / Ruzyla, K. / Bashtannyk-Puhalovich, T.A. / Kim, N. / Worrall, D.M. / Rossjohn, J. / Whisstock, J.C.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: The high resolution crystal structure of the human tumor suppressor maspin reveals a novel conformational switch in the G-helix.
Authors: Law, R.H. / Irving, J.A. / Buckle, A.M. / Ruzyla, K. / Buzza, M. / Bashtannyk-Puhalovich, T.A. / Beddoe, T.C. / Nguyen, K. / Worrall, D.M. / Bottomley, S.P. / Bird, P.I. / Rossjohn, J. / Whisstock, J.C.
History
DepositionOct 25, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Maspin
B: Maspin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,5804
Polymers85,3882
Non-polymers1922
Water2,216123
1
A: Maspin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8863
Polymers42,6941
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Maspin


Theoretical massNumber of molelcules
Total (without water)42,6941
Polymers42,6941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.540, 100.480, 136.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUASPASPAA4 - 3329 - 337
21LEULEUASPASPBB4 - 3329 - 337
12HISHISPROPROAA344 - 375349 - 380
22HISHISPROPROBB344 - 375349 - 380

NCS ensembles :
ID
1
2
DetailsThe biological unit consists of a monomer.

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Components

#1: Protein Maspin / Protease inhibitor 5


Mass: 42693.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINB5 / Plasmid: pRSETC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P36952
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.1 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: Ammonium sulfate, Bis-Tris, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 15, 2004 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 18753 / Num. obs: 18174 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 11.5
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1711 / % possible all: 93.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNS1refinement
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OVA CHAIN A

1ova


Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.859 / SU B: 37.851 / SU ML: 0.373 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.483 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28568 945 5.2 %RANDOM
Rwork0.2207 ---
obs0.22409 17231 96.91 %-
all-18753 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK / Bsol: 31.05 Å2 / ksol: 0.325 e/Å3
Displacement parametersBiso mean: 43.129 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å20 Å2
2--1.2 Å20 Å2
3----1.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.81 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5815 0 10 123 5948
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225927
X-RAY DIFFRACTIONr_angle_refined_deg1.281.9717988
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1635734
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.78426.231260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.733151129
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2271511
X-RAY DIFFRACTIONr_chiral_restr0.0870.2911
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024341
X-RAY DIFFRACTIONr_nbd_refined0.2260.22740
X-RAY DIFFRACTIONr_nbtor_refined0.3110.24005
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2251
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2650.2103
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.380.215
X-RAY DIFFRACTIONr_mcbond_it1.07133771
X-RAY DIFFRACTIONr_mcangle_it1.88955977
X-RAY DIFFRACTIONr_scbond_it3.18872361
X-RAY DIFFRACTIONr_scangle_it5.045102011
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
12578tight positional0.040.05
2275tight positional0.040.05
12578tight thermal0.080.5
2275tight thermal0.090.5
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 55 -
Rwork0.307 1150 -
obs--90.26 %

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