[English] 日本語
Yorodumi
- PDB-1z1x: Crystal Structure of a novel disintegrin from Saw-scaled viper at... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1z1x
TitleCrystal Structure of a novel disintegrin from Saw-scaled viper at 3.2 A resolution
Componentsdisintegrin
KeywordsPROTEIN BINDING / DISINTEGRIN / SAW-SCALED VIPER
Function / homology
Function and homology information


toxin activity / extracellular region
Similarity search - Function
Disintegrin domain / Echistatin / Disintegrin, conserved site / Disintegrins signature. / Disintegrin / Disintegrin domain profile. / Homologues of snake disintegrins / Disintegrin domain / Disintegrin domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Biological speciesEchis carinatus (saw-scaled viper)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsHassan, M.I. / Ethayathulla, A.S. / Bilgrami, S. / Singh, B. / Yadav, S. / Singh, T.P.
CitationJournal: To be published
Title: Crystal Structure of a novel disintegrin from Saw-scaled viper at 3.2A resolution
Authors: Hassan, M.I. / Ethayathulla, A.S. / Bilgrami, S. / Singh, B. / Yadav, S. / Singh, T.P.
History
DepositionMar 7, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: disintegrin


Theoretical massNumber of molelcules
Total (without water)7,1391
Polymers7,1391
Non-polymers00
Water1448
1
A: disintegrin

A: disintegrin


Theoretical massNumber of molelcules
Total (without water)14,2782
Polymers14,2782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x+1/2,y,-z+3/41
Unit cell
Length a, b, c (Å)91.368, 91.368, 54.941
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

-
Components

#1: Protein disintegrin


Mass: 7139.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echis carinatus (saw-scaled viper) / Secretion: Venom / Strain: Saw-scaled Viper / References: UniProt: Q5EE07
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4 Å3/Da / Density % sol: 70 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1.2M AMMONIUM SULFATE, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 10, 2005 / Details: MIRROR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→64.55 Å / Num. all: 2062 / Num. obs: 2058 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 55.2 Å2 / Rsym value: 0.2 / Net I/σ(I): 8.3
Reflection shellResolution: 3.2→3.32 Å / Mean I/σ(I) obs: 3.9 / Num. unique all: 191 / Rsym value: 0.544 / % possible all: 97.6

-
Processing

Software
NameVersionClassification
REFMAC5refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1rmr

1rmr


Resolution: 3.2→64 Å / Cor.coef. Fo:Fc: 0.873 / Cor.coef. Fo:Fc free: 0.821 / SU B: 27.591 / SU ML: 0.486 / Cross valid method: THROUGHOUT / ESU R Free: 0.442 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2648 91 4.4 %RANDOM
Rwork0.23432 ---
all0.236 2058 --
obs0.23594 1967 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 50.852 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å20 Å2
2--0.79 Å20 Å2
3----1.58 Å2
Refinement stepCycle: LAST / Resolution: 3.2→64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms490 0 0 8 498
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.021505
X-RAY DIFFRACTIONr_bond_other_d0.0020.02418
X-RAY DIFFRACTIONr_angle_refined_deg2.351.957684
X-RAY DIFFRACTIONr_angle_other_deg1.4143985
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.343363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.1491580
X-RAY DIFFRACTIONr_chiral_restr0.1370.270
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.02570
X-RAY DIFFRACTIONr_gen_planes_other0.0060.0299
X-RAY DIFFRACTIONr_nbd_refined0.2760.3114
X-RAY DIFFRACTIONr_nbd_other0.2840.3434
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.530
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0380.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5380.317
X-RAY DIFFRACTIONr_symmetry_vdw_other0.4190.348
X-RAY DIFFRACTIONr_mcbond_it1.6521.5320
X-RAY DIFFRACTIONr_mcangle_it3.1162516
X-RAY DIFFRACTIONr_scbond_it4.073185
X-RAY DIFFRACTIONr_scangle_it7.2734.5168
LS refinement shellResolution: 3.202→3.285 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.176 7
Rwork0.328 131
obs-131

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more