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- PDB-4j4m: Crystal structure of TM-1, a Trimeresurus mucrosquamatus venom me... -

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Basic information

Entry
Database: PDB / ID: 4j4m
TitleCrystal structure of TM-1, a Trimeresurus mucrosquamatus venom metalloproteinase
Componentszinc-dependent metalloproteinase
KeywordsHYDROLASE / alpha/beta-mixed fold / endopeptidase
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / extracellular region / metal ion binding
Similarity search - Function
Reprolysin domain, adamalysin-type / Reprolysin (M12B) family zinc metalloprotease / 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
Snake venom metalloproteinase TM-1
Similarity search - Component
Biological speciesProtobothrops mucrosquamatus (Chinese habu)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChou, T.L. / Wu, C.H. / Huang, K.F. / Wang, A.H.
CitationJournal: Toxicon / Year: 2013
Title: Crystal structure of a Trimeresurus mucrosquamatus venom metalloproteinase providing new insights into the inhibition by endogenous tripeptide inhibitors.
Authors: Chou, T.L. / Wu, C.H. / Huang, K.F. / Wang, A.H.
History
DepositionFeb 7, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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

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Assembly

Deposited unit
A: zinc-dependent metalloproteinase
B: zinc-dependent metalloproteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0128
Polymers43,6192
Non-polymers3926
Water9,494527
1
A: zinc-dependent metalloproteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0715
Polymers21,8101
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: zinc-dependent metalloproteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9403
Polymers21,8101
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.766, 80.766, 120.451
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein zinc-dependent metalloproteinase


Mass: 21809.641 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Protobothrops mucrosquamatus (Chinese habu)
References: UniProt: U3KRG1*PLUS, trimerelysin II
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 527 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. AUTHOR STATES THIS PROTEIN WAS ...A SEQUENCE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. AUTHOR STATES THIS PROTEIN WAS NATURALLY PURIFIED FROM SNAKE VENOM AND ITS AMINO-ACID SEQUENCE WAS DEDUCED FROM N-TERMINAL AND INTERNAL SEQUENCING, THE FINALLY-REFINED ELECTRON DENSITY MAPS, AND MULTIPLE SEQUENCE ALIGNMENT.

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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: 2.6 Å3/Da / Density % sol: 52.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG MME 550, 0.01 M zinc sulfate, 0.1M Mes, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 19, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. all: 41274 / Num. obs: 41233 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 33.4
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 3 / Num. unique all: 4107 / Rsym value: 0.615 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KUF

1kuf


Resolution: 1.8→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.207 1979 RANDOM
Rwork0.184 --
all0.195 39461 -
obs0.188 39461 -
Refinement stepCycle: LAST / Resolution: 1.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2980 0 6 527 3513
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.39
LS refinement shellResolution: 1.8→1.847 Å
RfactorNum. reflection% reflection
Rfree0.365 149 -
Rwork0.336 --
obs-2835 99.83 %

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