[English] 日本語
Yorodumi
- PDB-1bio: HUMAN COMPLEMENT FACTOR D IN COMPLEX WITH ISATOIC ANHYDRIDE INHIBITOR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bio
TitleHUMAN COMPLEMENT FACTOR D IN COMPLEX WITH ISATOIC ANHYDRIDE INHIBITOR
ComponentsCOMPLEMENT FACTOR DFactor D
KeywordsSERINE PROTEASE / HYDROLASE / COMPLEMENT / FACTOR D / CATALYTIC TRIAD / SELF-REGULATION
Function / homology
Function and homology information


complement factor D / Alternative complement activation / complement activation, alternative pathway / complement activation / Notch signaling pathway / platelet alpha granule lumen / serine-type peptidase activity / platelet degranulation / Platelet degranulation / secretory granule lumen ...complement factor D / Alternative complement activation / complement activation, alternative pathway / complement activation / Notch signaling pathway / platelet alpha granule lumen / serine-type peptidase activity / platelet degranulation / Platelet degranulation / secretory granule lumen / ficolin-1-rich granule lumen / proteolysis / serine-type endopeptidase activity / Neutrophil degranulation / neutrophil degranulation / extracellular exosome / extracellular region
Similarity search - Function
Complement factor D / Serine proteases, trypsin family, histidine 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 family, serine active site. / Serine proteases, trypsin domain / Trypsin ...Complement factor D / Serine proteases, trypsin family, histidine 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 family, serine active site. / 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
ISATOIC ANHYDRIDE / Complement factor D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsJing, H. / Babu, Y.S. / Moore, D. / Kilpatrick, J.M. / Liu, X.-Y. / Volanakis, J.E. / Narayana, S.V.L.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Structures of native and complexed complement factor D: implications of the atypical His57 conformation and self-inhibitory loop in the regulation of specific serine protease activity.
Authors: Jing, H. / Babu, Y.S. / Moore, D. / Kilpatrick, J.M. / Liu, X.Y. / Volanakis, J.E. / Narayana, S.V.
#1: Journal: Protein Sci. / Year: 1996
Title: Complement Factor D, a Novel Serine Protease
Authors: Volanakis, J.E. / Narayana, S.V.
#2: 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.
#3: Journal: J.Biol.Chem. / Year: 1995
Title: Erratum. Crystal Structure of a Complement Factor D Mutant Expressing Enhanced Catalytic Activity
Authors: Kim, S. / Narayana, S.V. / Volanakis, J.E.
#4: 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.
#5: 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
DepositionJun 18, 1998Processing site: BNL
Revision 1.0Jun 22, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: COMPLEMENT FACTOR D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6543
Polymers24,4391
Non-polymers2152
Water5,152286
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)55.480, 49.910, 39.430
Angle α, β, γ (deg.)90.00, 105.69, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein COMPLEMENT FACTOR D / Factor D


Mass: 24438.807 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ISATOIC ANHYDRIDE ACYLATES ACTIVE SITE SER 195 / Source: (natural) Homo sapiens (human) / References: UniProt: P00746, complement factor D
#2: Chemical ChemComp-SOA / ISATOIC ANHYDRIDE / Isatoic anhydride


Mass: 123.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9NO
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 44 %
Crystal growpH: 6.4 / Details: pH 6.4
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
18-10 mg/mlprotein1drop
210 mMTris-HCl1drop
30.1 M1dropNaCl
514-16 %(w/v)PEG60001reservoir
650 mMMES1reservoir
710 %DMSO1reservoir
4DMSO-dissolved IA1dropa molar ratio of 20:1

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 1997 / Details: MIRRORS
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 31552 / % possible obs: 95 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 29
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 4 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 5.5 / % possible all: 90
Reflection
*PLUS
Num. measured all: 133846
Reflection shell
*PLUS
% possible obs: 90 %

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DSU MOLECULE B
Resolution: 1.5→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT CORRECTION WAS APPLIED
RfactorNum. reflection% reflectionSelection details
Rfree0.191 3159 10 %RANDOM
Rwork0.186 ---
obs0.186 31181 94 %-
Displacement parametersBiso mean: 17.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1712 0 15 286 2013
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.564
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.57
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.169
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.5→1.57 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.325 349 10 %
Rwork0.303 3166 -
obs--85 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2ISA.PARTOPH19.SOL
X-RAY DIFFRACTION3GLC.PARTOPH19.PEP
X-RAY DIFFRACTION4ISA.TOP & GLC.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.57
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.169

+
About Yorodumi

-
News

-
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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
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