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- PDB-4aju: Crystal structure of the reactive loop cleaved ZPI in P41 space group -

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Basic information

Entry
Database: PDB / ID: 4aju
TitleCrystal structure of the reactive loop cleaved ZPI in P41 space group
Components(PROTEIN Z-DEPENDENT PROTEASE INHIBITOR) x 2
KeywordsBLOOD CLOTTING / SERPIN / PROTEIN Z / ZPI COAGULATION
Function / homology
Function and homology information


Post-translational protein phosphorylation / serine-type endopeptidase inhibitor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / heparin binding / endoplasmic reticulum lumen / extracellular space / extracellular exosome
Similarity search - Function
Protein Z-dependent peptidase inhibitor, serpin domain / Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 ...Protein Z-dependent peptidase inhibitor, serpin domain / Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / 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
Protein Z-dependent protease inhibitor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsZhou, A. / Yan, Y. / Wei, Z.
CitationJournal: Blood / Year: 2012
Title: Structural Basis for Catalytic Activation of Protein Z-Dependent Protease Inhibitor (Zpi) by Protein Z.
Authors: Huang, X. / Yan, Y. / Tu, Y. / Gatti, J. / Broze, G.J.J. / Zhou, A. / Olson, S.T.
History
DepositionFeb 19, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Other
Category: citation_author / pdbx_database_proc / pdbx_database_status
Item: _citation_author.name / _pdbx_database_status.recvd_author_approval
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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: PROTEIN Z-DEPENDENT PROTEASE INHIBITOR
B: PROTEIN Z-DEPENDENT PROTEASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9717
Polymers48,5252
Non-polymers4465
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-83 kcal/mol
Surface area19010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.698, 100.698, 78.972
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 PROTEIN Z-DEPENDENT PROTEASE INHIBITOR / PZ-DEPENDENT PROTEASE INHIBITOR / PZI / SERPIN A10


Mass: 44357.996 Da / Num. of mol.: 1 / Fragment: RESIDUES 23-408 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: REACTIVE LOOP CLEAVED ZPI / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PSUMO3-HZPI-Y387R / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: Q9UK55
#2: Protein/peptide PROTEIN Z-DEPENDENT PROTEASE INHIBITOR / PZ-DEPENDENT PROTEASE INHIBITOR / PZI / SERPIN A10


Mass: 4167.010 Da / Num. of mol.: 1 / Fragment: RESIDUES 409-444 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: REACTIVE LOOP CLEAVED ZPI / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PSUMO3-HZPI-Y387R / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: Q9UK55
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.07 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 4.5 / Details: 10% 2-PROPANOL, 0.2M LI2SO4, 0.1M NAAC, PH4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→100.26 Å / Num. obs: 22072 / % possible obs: 95.8 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.9
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.5 / % possible all: 82.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0099refinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 7API

7api


Resolution: 2.65→100.5 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.923 / SU B: 22.72 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.362 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25766 1127 5.1 %RANDOM
Rwork0.21542 ---
obs0.21754 20932 95.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.299 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å20 Å20 Å2
2--1.06 Å20 Å2
3----2.12 Å2
Refinement stepCycle: LAST / Resolution: 2.65→100.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3114 0 24 10 3148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223199
X-RAY DIFFRACTIONr_bond_other_d0.0010.022257
X-RAY DIFFRACTIONr_angle_refined_deg1.0211.984302
X-RAY DIFFRACTIONr_angle_other_deg0.74335490
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8165381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.46323.451142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.115601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2521522
X-RAY DIFFRACTIONr_chiral_restr0.0610.2475
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213430
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02661
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_it0.381.51917
X-RAY DIFFRACTIONr_mcbond_other0.0391.5772
X-RAY DIFFRACTIONr_mcangle_it0.73623100
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.90831282
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.6034.51202
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.433 58 -
Rwork0.393 1179 -
obs--72.38 %
Refinement TLS params.

T33: 0.0808 Å2 / 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)Origin x (Å)Origin y (Å)Origin z (Å)
13.138-0.32481.43971.6092-0.21043.64920.1232-0.0198-0.1606-0.064-0.02750.31060.1485-0.3115-0.09570.0729-0.04750.01660.074-0.027132.2906-2.9048-0.5229
25.6271-1.74332.45172.2258-1.27696.323-0.1055-0.4380.16040.1934-0.06960.2413-0.0686-0.29550.17510.1358-0.0430.05490.1318-0.035941.14980.339112.4569
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 386
2X-RAY DIFFRACTION2B388 - 423

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