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- PDB-3ndd: Cleaved antitrypsin with P10 Pro, and P9-P6 Asp -

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Basic information

Entry
Database: PDB / ID: 3ndd
TitleCleaved antitrypsin with P10 Pro, and P9-P6 Asp
Components(Alpha-1-antitrypsin) x 2
KeywordsHYDROLASE INHIBITOR / serpin
Function / homology
Function and homology information


Cargo concentration in the ER / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / acute-phase response / 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 ...Cargo concentration in the ER / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / acute-phase response / 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 / Platelet degranulation / protease binding / collagen-containing extracellular matrix / ficolin-1-rich granule lumen / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / Neutrophil degranulation / Golgi apparatus / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding
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: 1.5 Å
AuthorsYamasaki, M. / Sendall, T.J. / Huntington, J.A.
CitationJournal: J. Biol. Chem. / Year: 2010
Title: Loop-sheet mechanism of serpin polymerization tested by reactive center loop mutations
Authors: Yamasaki, M. / Sendall, T.J. / Harris, L.E. / Lewis, G.M.W. / Huntington, J.A.
History
DepositionJun 7, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 28, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Nov 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: Alpha-1-antitrypsin
B: Alpha-1-antitrypsin


Theoretical massNumber of molelcules
Total (without water)42,7692
Polymers42,7692
Non-polymers00
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-36 kcal/mol
Surface area14990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.230, 121.880, 43.220
Angle α, β, γ (deg.)90.00, 113.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alpha-1-antitrypsin / Alpha-1 protease inhibitor / Alpha-1-antiproteinase / Serpin A1 / Short peptide from AAT / SPAAT


Mass: 38628.676 Da / Num. of mol.: 1
Fragment: P1 cleaved antitrypsin, nterm, UNP residues 46-382
Mutation: C232A, G349P, A350D, M351D, F352D, L353D, M358R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA1, AAT, PI, PRO0684, PRO2209 / Plasmid: pCEP4 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: P01009
#2: Protein/peptide Alpha-1-antitrypsin / Alpha-1 protease inhibitor / Alpha-1-antiproteinase / Serpin A1 / Short peptide from AAT / SPAAT


Mass: 4139.938 Da / Num. of mol.: 1
Fragment: P1 cleaved antitrypsin, cterm, UNP residues 383-418
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA1, AAT, PI, PRO0684, PRO2209 / Plasmid: pCEP4 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: P01009
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 41.33 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6
Details: 0.1M MES/NaOH, 30% PEG 400, 35% glycerol, pH 6, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 4, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→34.04 Å / Num. all: 55516 / Num. obs: 55516 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 10.4
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2.4 / Num. unique all: 8057 / Rsym value: 0.496 / % possible all: 98.8

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.5.0088refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EZX

1ezx


Resolution: 1.5→32.79 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.032 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21118 2822 5.1 %RANDOM
Rwork0.15977 ---
obs0.16235 52634 98.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.412 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0 Å20.02 Å2
2---0.04 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.5→32.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2882 0 0 216 3098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0223051
X-RAY DIFFRACTIONr_angle_refined_deg2.0831.9634160
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5955393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.77325.704135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.44515522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.797157
X-RAY DIFFRACTIONr_chiral_restr0.1510.2482
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212320
X-RAY DIFFRACTIONr_mcbond_it2.3771.51922
X-RAY DIFFRACTIONr_mcangle_it3.48723124
X-RAY DIFFRACTIONr_scbond_it4.82831129
X-RAY DIFFRACTIONr_scangle_it6.9254.51036
X-RAY DIFFRACTIONr_rigid_bond_restr2.80633051
X-RAY DIFFRACTIONr_sphericity_free12.3953216
X-RAY DIFFRACTIONr_sphericity_bonded7.17532979
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 197 -
Rwork0.258 3879 -
obs--98.57 %

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