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- PDB-4afx: Crystal structure of the reactive loop cleaved ZPI in I2 space group -

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Basic information

Entry
Database: PDB / ID: 4afx
TitleCrystal structure of the reactive loop cleaved ZPI in I2 space group
Components(PROTEIN Z DEPENDENT PROTEASE ...) x 2
KeywordsHYDROLASE INHIBITOR / SERPIN / PROTEIN Z DEPENDENT INHIBITOR / 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
PHOSPHATE ION / Protein Z-dependent protease inhibitor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 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
DepositionJan 23, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other
Category: citation_author / pdbx_database_proc ...citation_author / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _citation_author.name / _pdbx_database_status.recvd_author_approval
Revision 1.2Dec 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)48,8968
Polymers48,5252
Non-polymers3716
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-81.1 kcal/mol
Surface area17200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.850, 106.660, 81.163
Angle α, β, γ (deg.)90.00, 112.58, 90.00
Int Tables number5
Space group name H-MI121

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Components

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PROTEIN Z DEPENDENT PROTEASE ... , 2 types, 2 molecules AB

#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

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Non-polymers , 4 types, 33 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, TYR 408 TO ARG ENGINEERED RESIDUE IN CHAIN B, TYR 408 TO ARG

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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: 3.25 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 5 / Details: 1.8M NAK PHOSPHATE, PH5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / 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: 2.09→44.39 Å / Num. obs: 31054 / % possible obs: 84.3 % / Observed criterion σ(I): 2 / Redundancy: 87 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.9
Reflection shellResolution: 2.09→2.2 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.8 / % possible all: 87

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 7API

7api


Resolution: 2.09→66.52 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU B: 9.127 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24882 1573 5.1 %RANDOM
Rwork0.20953 ---
obs0.21151 29436 84.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.827 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å20 Å21.34 Å2
2---0.49 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.09→66.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3083 0 18 27 3128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223160
X-RAY DIFFRACTIONr_bond_other_d0.0010.022233
X-RAY DIFFRACTIONr_angle_refined_deg1.5411.9794256
X-RAY DIFFRACTIONr_angle_other_deg0.86235428
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9195379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.4623.309139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.87815592
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3751522
X-RAY DIFFRACTIONr_chiral_restr0.0870.2471
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213408
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02659
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_it0.8831.51899
X-RAY DIFFRACTIONr_mcbond_other0.1851.5768
X-RAY DIFFRACTIONr_mcangle_it1.65823075
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.40631261
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9714.51181
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: 2.086→2.14 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 118 -
Rwork0.317 2239 -
obs--86.43 %
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)
11.57880.7292-0.35071.2909-0.52041.1625-0.00590.00970.0332-0.0222-0.0050.0441-0.07280.05080.0110.02480.00370.0060.0446-0.0260.03316.4048-17.29827.4469
20.7983-0.0141-0.07612.3058-1.41742.4884-0.04940.05480.0778-0.1182-0.0231-0.147-0.04830.11440.07250.0315-0.02410.00140.02730.00290.035615.3097-6.448822.0197
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A40 - 386
2X-RAY DIFFRACTION2B390 - 423

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