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- PDB-1qmn: Alpha1-antichymotrypsin serpin in the delta conformation (partial... -

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Basic information

Entry
Database: PDB / ID: 1qmn
TitleAlpha1-antichymotrypsin serpin in the delta conformation (partial loop insertion)
ComponentsALPHA-1-ANTICHYMOTRYPSINAlpha 1-antichymotrypsin
KeywordsHYDROLASE INHIBITOR / SERPIN / SERINE PROTEINASE INHIBITOR / HYDROLASE INHIBITOR LOOP-SHEET POLYMERIZATION / EMPHYSEMA / DISEASE MUTATION / ACUTE PHASE PROTEIN / CONFORMATIONAL DISEASE
Function / homology
Function and homology information


maintenance of gastrointestinal epithelium / regulation of lipid metabolic process / platelet alpha granule lumen / acute-phase response / serine-type endopeptidase inhibitor activity / azurophil granule lumen / Platelet degranulation / secretory granule lumen / collagen-containing extracellular matrix / blood microparticle ...maintenance of gastrointestinal epithelium / regulation of lipid metabolic process / platelet alpha granule lumen / acute-phase response / serine-type endopeptidase inhibitor activity / azurophil granule lumen / Platelet degranulation / secretory granule lumen / collagen-containing extracellular matrix / blood microparticle / inflammatory response / Neutrophil degranulation / DNA binding / extracellular space / extracellular exosome / extracellular region / nucleus
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
Alpha-1-antichymotrypsin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsGooptu, B. / Hazes, B. / Lomas, D.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Inactive Conformation of the Serpin Alpha1-Antichymotrypsin Indicates Two-Stage Insertion of the Reactive Loop: Implications for Inhibitory Function and Conformational Disease
Authors: Gooptu, B. / Hazes, B. / Chang, W.-S.W. / Dafforn, T.R. / Carrell, R.W. / Read, R.J. / Lomas, D.A.
History
DepositionOct 4, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2000Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-1-ANTICHYMOTRYPSIN


Theoretical massNumber of molelcules
Total (without water)45,3541
Polymers45,3541
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.723, 122.094, 41.724
Angle α, β, γ (deg.)90.00, 101.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ALPHA-1-ANTICHYMOTRYPSIN / Alpha 1-antichymotrypsin / AACT / ACT / CELL GROWTH-INHIBITING GENE 24/25 PROTEIN / SERPIN A3 / ALPHA-1-ANTICHYMOTRYPSIN HIS-PRO-LESS


Mass: 45353.691 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: BLOOD PLASMA / Description: THE MUTATION IS A NATURALLY OCCURRING VARIANT / Plasmid: PZM-S / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): N4830-1 / References: UniProt: P01011
Compound detailsRESIDUE 55 HAS BEEN MUTATED FROM LEU TO PRO. THIS MUTANT IS A NATURALLY OCCURRING VARIANT WHICH HAS ...RESIDUE 55 HAS BEEN MUTATED FROM LEU TO PRO. THIS MUTANT IS A NATURALLY OCCURRING VARIANT WHICH HAS BEEN ASSOCIATED WITH PLASMA DEFICIENCY AND CHRONIC OBSTRUCTIVE PULMONARY DISEASE.
Sequence detailsMET 0, PART OF EXPRESSION VECTOR ALA 1, PART OF EXPRESSION VECTOR SER 2, PART OF EXPRESSION VECTOR ...MET 0, PART OF EXPRESSION VECTOR ALA 1, PART OF EXPRESSION VECTOR SER 2, PART OF EXPRESSION VECTOR RESIDUES THR 226A AND LEU 278A ARE NUMBERED WITH AN INSERT CODE TO MATCH THE RESIDUE NUMBERING IN PDB ENTRY 1AS4

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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: 2.31 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 1 MICROLITER OF 10MG/ML PROTEIN IN 50MM TRIS, 50MM KCL, PH 7.4 WAS MIXED WITH 2 MICROLITER OF PRECIPITANT AND EQUILIBRATED AS A HANGING DROP OVER 1ML OF PRECIPITANT (20% [W/V] PEG 4000, 0.2M ...Details: 1 MICROLITER OF 10MG/ML PROTEIN IN 50MM TRIS, 50MM KCL, PH 7.4 WAS MIXED WITH 2 MICROLITER OF PRECIPITANT AND EQUILIBRATED AS A HANGING DROP OVER 1ML OF PRECIPITANT (20% [W/V] PEG 4000, 0.2M AMMONIUM SULPHATE, 0.1M NAOAC, PH 4.5), AT 18 DEGREES C
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
250 mMTris1drop
350 mM1dropKCl
420 %(w/v)PEG40001reservoir
50.2 Mammonium sulfate1reservoir
60.1 M1reservoirNaOAc

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.448
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.448 Å / Relative weight: 1
ReflectionResolution: 2.3→41 Å / Num. obs: 11373 / % possible obs: 62.1 % / Redundancy: 1.7 % / Biso Wilson estimate: 34.3 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.101 / Net I/σ(I): 4.4
Reflection shellResolution: 2.27→2.39 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.343 / % possible all: 17.2
Reflection
*PLUS
Num. measured all: 18805

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Processing

Software
NameVersionClassification
CNS0.5refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AS4

1as4


Resolution: 2.27→40.95 Å / Data cutoff high absF: 1393995.53 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
Details: RESIDUES 86-89, 104-110, 122-125, AND 212-214 HAD VERY WEAK DENSITY. THEY HAVE BEEN LEFT IN THE CONFORMATION OF THE MOLECULAR REPLACEMENT SEARCH MODEL (1AS4) WHICH WAS DETERMINED AT HIGHER ...Details: RESIDUES 86-89, 104-110, 122-125, AND 212-214 HAD VERY WEAK DENSITY. THEY HAVE BEEN LEFT IN THE CONFORMATION OF THE MOLECULAR REPLACEMENT SEARCH MODEL (1AS4) WHICH WAS DETERMINED AT HIGHER RESOLUTION. HOWEVER, STEREOCHEMICAL PROBLEMS DO OCCUR IN THESE REGIONS. THE DENSITY FOR THE SIDE CHAIN ATOMS OF RESIDUES: LYS 162, ILE 173, SER 348, THR 351, LEU 358 AND SER 359 WAS ABSENT. THEREFORE NO ATOMS BEYOND CB HAVE BEEN INCLUDED IN THE MODEL. ALA 398 WAS NOT VISIBLE IN THE DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1036 9.1 %RANDOM
Rwork0.197 ---
obs0.197 11373 60 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.66 Å2 / ksol: 0.3014 e/Å3
Displacement parametersBiso mean: 40.9 Å2
Baniso -1Baniso -2Baniso -3
1--5.487 Å20 Å2-3.606 Å2
2--5.005 Å20 Å2
3---0.482 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.29 Å
Luzzati d res low-500 Å
Luzzati sigma a0.33 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.27→40.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2897 0 0 0 2897
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.036
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_deg2.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.060.015
X-RAY DIFFRACTIONc_mcangle_it3.550.03
X-RAY DIFFRACTIONc_scbond_it7.570.045
X-RAY DIFFRACTIONc_scangle_it10.260.09
LS refinement shellResolution: 2.27→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3725 11 9.1 %
Rwork0.2973 72 -
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75

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