[English] 日本語
Yorodumi
- PDB-1dst: MUTANT OF FACTOR D WITH ENHANCED CATALYTIC ACTIVITY -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1dst
TitleMUTANT OF FACTOR D WITH ENHANCED CATALYTIC ACTIVITY
ComponentsFACTOR D
KeywordsHYDROLASE (SERINE PROTEASE) / COMPLEMENT ACTIVATING ENZYME / HYDROLASE / SERINE PROTEASE / FACTOR D
Function / homology
Function and homology information


complement factor D / Alternative complement activation / complement activation, alternative pathway / complement activation / serine-type peptidase activity / platelet alpha granule lumen / response to bacterium / Platelet degranulation / secretory granule lumen / ficolin-1-rich granule lumen ...complement factor D / Alternative complement activation / complement activation, alternative pathway / complement activation / serine-type peptidase activity / platelet alpha granule lumen / response to bacterium / Platelet degranulation / secretory granule lumen / ficolin-1-rich granule lumen / serine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular exosome / extracellular region
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsNarayana, S.V.L. / Volanakis, J.E.
Citation
Journal: J.Biol.Chem. / Year: 1995
Title: Crystal structure of a complement factor D mutant expressing enhanced catalytic activity.
Authors: Kim, S. / Narayana, S.V. / Volanakis, J.E.
#1: Journal: J.Immunol. / Year: 1995
Title: Catalytic Role of a Surface Loop of the Complement Serine Protease Factor D
Authors: Kim, S. / Narayana, S.V. / Volanakis, J.E.
#2: Journal: Biochemistry / Year: 1994
Title: Mutational Analysis of the Substrate Binding Site of Human Complement Factor D
Authors: Kim, S. / Narayana, S.V. / Volanakis, J.E.
#3: Journal: J.Mol.Biol. / Year: 1994
Title: Structure of Human Factor D. A Complement System Protein at 2.0 A Resolution
Authors: Narayana, S.V. / Carson, M. / El-Kabbani, O. / Kilpatrick, J.M. / Moore, D. / Chen, X. / Bugg, C.E. / Volanakis, J.E. / Delucas, L.J.
#4: Journal: J.Mol.Biol. / Year: 1991
Title: Crystallization and Preliminary X-Ray Investigation of Factor D of Human Complement
Authors: Narayana, S.V. / Kilpatrick, J.M. / El-Kabbani, O. / Babu, Y.S. / Bugg, C.E. / Volanakis, J.E. / Delucas, L.J.
History
DepositionSep 13, 1995Processing site: BNL
Revision 1.0Jul 11, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FACTOR D


Theoretical massNumber of molelcules
Total (without water)24,6001
Polymers24,6001
Non-polymers00
Water1,09961
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.380, 45.380, 175.210
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein FACTOR D /


Mass: 24600.008 Da / Num. of mol.: 1 / Mutation: S94Y, T214S, S215W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: OVARY / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P00746, complement factor D
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42 %
Crystal growpH: 6.8 / Details: pH 6.8
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mMMES1reservoir
2PEG60001reservoir

-
Data collection

DiffractionMean temperature: 295 K
Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 14652 / % possible obs: 94 % / Observed criterion σ(I): 1.5 / Redundancy: 6 % / Rmerge(I) obs: 0.076
Reflection
*PLUS
Num. all: 14652 / Num. obs: 13899 / Num. measured all: 59734

-
Processing

Software
NameClassification
XENGENdata collection
XENGENdata reduction
PROLSQrefinement
XENGENdata scaling
RefinementResolution: 2→7.5 Å / σ(F): 1.5
Details: THERE IS NO DENSITY FOR THE LOOP 171 TO 175, HENCE THEIR PSI, PHI VALUES ARE OUT OF THE ALLOWED REGIONS IN THE RAMACHANDRAN PLOT.
RfactorNum. reflection
Rfree0.213 -
obs-13311
Displacement parametersBiso mean: 15.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 2→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1784 0 0 57 1841
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.025
X-RAY DIFFRACTIONp_angle_d0.0350.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0560.065
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.011.5
X-RAY DIFFRACTIONp_mcangle_it1.542
X-RAY DIFFRACTIONp_scbond_it1.652
X-RAY DIFFRACTIONp_scangle_it2.12.5
X-RAY DIFFRACTIONp_plane_restr2.53.5
X-RAY DIFFRACTIONp_chiral_restr0.0340.05
X-RAY DIFFRACTIONp_singtor_nbd0.20.4
X-RAY DIFFRACTIONp_multtor_nbd0.1910.4
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1330.4
X-RAY DIFFRACTIONp_planar_tor2.4
X-RAY DIFFRACTIONp_staggered_tor21.315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor16.520
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.198 / Rfactor Rwork: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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