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- PDB-1bio: HUMAN COMPLEMENT FACTOR D IN COMPLEX WITH ISATOIC ANHYDRIDE INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 1bio
TitleHUMAN COMPLEMENT FACTOR D IN COMPLEX WITH ISATOIC ANHYDRIDE INHIBITOR
ComponentsCOMPLEMENT FACTOR 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 / complement activation, alternative pathway / serine-type peptidase activity / platelet alpha granule lumen / protein maturation / response to bacterium / Platelet degranulation / secretory granule lumen ...complement factor D / Alternative complement activation / complement activation / complement activation, alternative pathway / serine-type peptidase activity / platelet alpha granule lumen / protein maturation / response to bacterium / Platelet degranulation / secretory granule lumen / ficolin-1-rich granule lumen / serine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / 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 / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / 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
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
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
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

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Components

#1: Protein COMPLEMENT 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


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


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


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

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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: 2.15 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

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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 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DSU MOLECULE B

1dsu


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

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