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- PDB-1kuf: High-resolution Crystal Structure of a Snake Venom Metalloprotein... -

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Basic information

Entry
Database: PDB / ID: 1kuf
TitleHigh-resolution Crystal Structure of a Snake Venom Metalloproteinase from Taiwan Habu
Componentsmetalloproteinase
KeywordsHYDROLASE / alpha/beta protein
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / toxin activity / proteolysis / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
Disintegrin, conserved site / Disintegrins signature. / Peptidase M12B, propeptide / Reprolysin family propeptide / Reprolysin domain, adamalysin-type / Reprolysin (M12B) family zinc metalloprotease / Disintegrin / Disintegrin domain profile. / Homologues of snake disintegrins / Disintegrin domain ...Disintegrin, conserved site / Disintegrins signature. / Peptidase M12B, propeptide / Reprolysin family propeptide / Reprolysin domain, adamalysin-type / Reprolysin (M12B) family zinc metalloprotease / Disintegrin / Disintegrin domain profile. / Homologues of snake disintegrins / Disintegrin domain / Disintegrin domain superfamily / Peptidase M12B, ADAM/reprolysin / ADAM type metalloprotease domain profile. / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Zinc metalloproteinase/disintegrin
Similarity search - Component
Biological speciesProtobothrops mucrosquamatus (Chinese habu)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsHuang, K.F. / Chiou, S.H. / Ko, T.P. / Yuann, J.M. / Wang, A.H.J.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: The 1.35 A structure of cadmium-substituted TM-3, a snake-venom metalloproteinase from Taiwan habu: elucidation of a TNFalpha-converting enzyme-like active-site structure with a distorted ...Title: The 1.35 A structure of cadmium-substituted TM-3, a snake-venom metalloproteinase from Taiwan habu: elucidation of a TNFalpha-converting enzyme-like active-site structure with a distorted octahedral geometry of cadmium.
Authors: Huang, K.F. / Chiou, S.H. / Ko, T.P. / Yuann, J.M. / Wang, A.H.
#1: Journal: Biochem.Biophys.Res.Commun. / Year: 1995
Title: Characterization of multiple metalloproteinases with fibrinogenolytic activity from the venom of Taiwan habu (Trimeresurus mucrosquamatus): protein microsequencing coupled with cDNA sequence analysis.
Authors: Huang, K.F. / Hung, C.C. / Pan, F.M. / Chow, L.P. / Tsugita, A. / Chiou, S.H.
History
DepositionJan 21, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: metalloproteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,50311
Polymers23,3791
Non-polymers1,12410
Water7,134396
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.991, 60.991, 128.398
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-360-

HOH

21A-641-

HOH

31A-653-

HOH

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Components

#1: Protein metalloproteinase / Atrolysin e


Mass: 23378.809 Da / Num. of mol.: 1 / Fragment: catalytic protease domain / Source method: isolated from a natural source
Source: (natural) Protobothrops mucrosquamatus (Chinese habu)
References: UniProt: O57413, EC: 3.4.24.44
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG400, sodium acetate, cadmium chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal grow
*PLUS
Temperature: 277 K / pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110.5 mg/mlprotein1drop
20.2 Mammonium acetate1droppH6.0
30.1 M1reservoirCdCl2
40.1 Msodium acetate1reservoir
530 %(v/v)PEG4001reservoirpH4.6

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11231
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONSPring-8 BL38B110.92
ROTATING ANODERIGAKU21.54
Detector
TypeIDDetectorDate
SIEMENS1CCDApr 19, 2001
RIGAKU RAXIS IV2IMAGE PLATESep 23, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.921
21.541
ReflectionResolution: 1.35→99 Å / Num. all: 113041 / Num. obs: 46914 / % possible obs: 86.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rmerge(I) obs: 0.057 / Rsym value: 0.02 / Net I/σ(I): 16.9
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 2.1 / Num. unique all: 4340 / % possible all: 82.2
Reflection
*PLUS
Lowest resolution: 99 Å / Num. measured all: 113041
Reflection shell
*PLUS
% possible obs: 82.2 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→30 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.204 2198 random
Rwork0.181 --
all0.252 43969 -
obs0.23 41770 -
Refinement stepCycle: LAST / Resolution: 1.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1616 0 10 396 2022
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.54
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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