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- PDB-3mz8: Crystal Structure of Zinc-Bound Natrin From Naja atra -

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Basic information

Entry
Database: PDB / ID: 3mz8
TitleCrystal Structure of Zinc-Bound Natrin From Naja atra
ComponentsNatrin-1
KeywordsTOXIN / NATRIN / CRISP / SERINE PROTEASE / ION CHANNEL BLOCKING / COBRA
Function / homology
Function and homology information


calcium channel regulator activity / potassium channel regulator activity / toxin activity / extracellular space
Similarity search - Function
Crisp domain / Cysteine-rich secretory protein / Cysteine-rich secretory protein, SCP domain / Crisp-like domain / Crisp / CRISP family signature 2. / Allergen V5/Tpx-1-related, conserved site / CRISP family signature 1. / Cysteine-rich secretory protein-related / ShKT domain ...Crisp domain / Cysteine-rich secretory protein / Cysteine-rich secretory protein, SCP domain / Crisp-like domain / Crisp / CRISP family signature 2. / Allergen V5/Tpx-1-related, conserved site / CRISP family signature 1. / Cysteine-rich secretory protein-related / ShKT domain / ShKT domain profile. / Pathogenesis-related Protein p14a / CAP / SCP / Tpx-1 / Ag5 / PR-1 / Sc7 family of extracellular domains. / CAP domain / Cysteine-rich secretory protein family / CAP superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Cysteine-rich venom protein natrin-1
Similarity search - Component
Biological speciesNaja atra (Chinese cobra)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWang, Y.L. / Hsieh, Y.C. / Liu, J.S. / Chen, C.J. / Wu, W.G.
Citation
Journal: J.Biol.Chem. / Year: 2010
Title: Cobra CRISP functions as an inflammatory modulator via a novel Zn2+- and heparan sulfate- dependent transcriptional regulation of endothelial cell adhesion molecules
Authors: Wang, Y.-L. / Kuo, J.-H. / Lee, S.-C. / Liu, J.-S. / Hsieh, Y.-C. / Shih, Y.-T. / Chen, C.-J. / Chiu, J.-J. / Wu, W.-G.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Purification, crystallization and preliminary X-ray crystallographic analysis of a cysteine-rich secretory protein (CRISP) from Naja atra venom
Authors: Wang, Y.-L. / Goh, K.-X. / Wu, W. / Chen, C.-J.
History
DepositionMay 12, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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

Downloads & links

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Assembly

Deposited unit
A: Natrin-1
B: Natrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0934
Polymers49,9622
Non-polymers1312
Water3,063170
1
A: Natrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0462
Polymers24,9811
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Natrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0462
Polymers24,9811
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.122, 65.539, 243.413
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Natrin-1 / natrin / Cysteine-rich venom protein 1 / NA-CRVP1 / Protein G2a


Mass: 24981.088 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Naja atra (Chinese cobra) / References: UniProt: Q7T1K6
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 20%(w/v) PEG 8000, 0.1M HEPES, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 29, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.54→30 Å / Num. obs: 15344 / % possible obs: 96.5 % / Observed criterion σ(I): 3.4 / Redundancy: 5.8 % / Rmerge(I) obs: 0.102 / Rsym value: 0.115 / Net I/σ(I): 13.9
Reflection shellResolution: 2.54→2.63 Å / Redundancy: 5 % / Rmerge(I) obs: 0.355 / Num. unique all: 1399 / Rsym value: 0.383 / % possible all: 90.6

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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: PDB ENTRY 1XTA

1xta


Resolution: 2.7→26.23 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2408 1272 9.6 %RANDOM
Rwork0.1826 11139 --
all-13224 --
obs-12411 93.9 %-
Solvent computationBsol: 26.222 Å2
Displacement parametersBiso max: 114.11 Å2 / Biso mean: 20 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1-8.201 Å20 Å20 Å2
2---3.947 Å20 Å2
3----4.255 Å2
Refinement stepCycle: LAST / Resolution: 2.7→26.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3476 0 2 170 3648
LS refinement shellResolution: 2.7→2.78 Å /
RfactorNum. reflection
Rfree0.24 -
Rwork0.182 -
obs-12411
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

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