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- PDB-2qug: Crystal structure of alpha-1-antitrypsin, crystal form A -

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Basic information

Entry
Database: PDB / ID: 2qug
TitleCrystal structure of alpha-1-antitrypsin, crystal form A
ComponentsAlpha-1-antitrypsin
KeywordsProtease Inhibitor / antitrypsin / polymerisation / protein aggregation / protein unfolding / serpin / Acute phase / Disease mutation / Glycoprotein / Secreted / Serine protease inhibitor
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 / collagen-containing extracellular matrix / protease binding / 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 / molecular replacement / Resolution: 2 Å
AuthorsHansen, G. / Morton, C.J. / Pearce, M.C. / Feil, S.C. / Adams, J.J. / Parker, M.W. / Bottomley, S.P.
CitationJournal: Protein Sci. / Year: 2008
Title: Preventing serpin aggregation: The molecular mechanism of citrate action upon antitrypsin unfolding.
Authors: Pearce, M.C. / Morton, C.J. / Feil, S.C. / Hansen, G. / Adams, J.J. / Parker, M.W. / Bottomley, S.P.
History
DepositionAug 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-1-antitrypsin


Theoretical massNumber of molelcules
Total (without water)44,4101
Polymers44,4101
Non-polymers00
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.368, 39.391, 90.154
Angle α, β, γ (deg.)90.00, 104.61, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Alpha-1-antitrypsin / Alpha-1 protease inhibitor / Alpha-1-antiproteinase


Mass: 44410.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA1, AAT, PI / Production host: Escherichia coli (E. coli) / References: UniProt: P01009
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.19 Å3/Da / Density % sol: 43.91 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 29% PEG 3350, 400 mM NaF, vapor diffusion, hanging drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 20, 2006
RadiationMonochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→87.37 Å / Num. obs: 24296 / % possible obs: 91.9 % / Redundancy: 4.8 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.139 / Rsym value: 0.139 / Net I/σ(I): 8.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.708 / Mean I/σ(I) obs: 2 / Num. measured all: 16785 / Num. unique all: 3426 / Rsym value: 0.708 / % possible all: 90.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.322 / Cor.coef. Fo:Fc: 0.762 / Cor.coef. Io to Ic: 0.751
Highest resolutionLowest resolution
Rotation3 Å15 Å
Translation3 Å15 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
AMoREphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→87.37 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.905 / SU B: 14.71 / SU ML: 0.19 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.232 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1225 5 %RANDOM
Rwork0.215 ---
obs0.218 24294 91.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.727 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å21.14 Å2
2--0.84 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 2→87.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2928 0 0 46 2974
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222988
X-RAY DIFFRACTIONr_bond_other_d00.022018
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.9714039
X-RAY DIFFRACTIONr_angle_other_deg0.79734976
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.5495368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.48625.672134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.39215547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.99157
X-RAY DIFFRACTIONr_chiral_restr0.0950.2464
X-RAY DIFFRACTIONr_gen_planes_refined0.0240.023268
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02565
X-RAY DIFFRACTIONr_nbd_refined0.2390.2582
X-RAY DIFFRACTIONr_nbd_other0.2410.22055
X-RAY DIFFRACTIONr_nbtor_refined0.1980.21381
X-RAY DIFFRACTIONr_nbtor_other0.0990.21654
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.272
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2760.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.350.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.24
X-RAY DIFFRACTIONr_mcbond_it2.871.52354
X-RAY DIFFRACTIONr_mcbond_other0.9351.5743
X-RAY DIFFRACTIONr_mcangle_it3.50522979
X-RAY DIFFRACTIONr_scbond_it5.43531312
X-RAY DIFFRACTIONr_scangle_it6.7924.51060
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 88 -
Rwork0.278 1642 -
all-1730 -
obs--91.1 %
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)
16.40320.0897-2.82631.41940.92367.2108-0.1413-0.51140.06840.00210.1865-0.1311-0.10610.0548-0.0452-0.1045-0.0646-0.02960.0349-0.0038-0.05529.0360.020932.6562
24.8230.38050.49272.72030.8524.3736-0.19840.1960.8082-0.36290.1039-0.0248-0.701-0.05040.09450.0023-0.0191-0.05210.13430.06880.100813.60021.68921.3356
34.49781.5981-2.49141.18-1.39072.5477-0.1115-0.0635-0.1121-0.1680.0596-0.06220.1184-0.08080.05190.0205-0.0272-0.0067-0.1163-0.0161-0.054535.8026-2.008317.8411
44.00961.1548-3.30934.0364-1.43695.99970.24140.4670.5445-0.61960.07270.223-0.4118-0.4428-0.31410.072-0.01810.0215-0.06510.0010.034142.4494.484710.9703
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA24 - 9824 - 98
2X-RAY DIFFRACTION2AA99 - 17099 - 170
3X-RAY DIFFRACTION3AA171 - 342171 - 342
4X-RAY DIFFRACTION4AA343 - 392343 - 392

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