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- PDB-1dfp: FACTOR D INHIBITED BY DIISOPROPYL FLUOROPHOSPHATE -

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Basic information

Entry
Database: PDB / ID: 1dfp
TitleFACTOR D INHIBITED BY DIISOPROPYL FLUOROPHOSPHATE
ComponentsFACTOR D
KeywordsSERINE PROTEASE / COMPLEMENT / FACTOR D / HYDROLASE
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
DIISOPROPYL PHOSPHONATE / Complement factor D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCole, L.B. / Chu, N. / Kilpatrick, J.M. / Volanakis, J.E. / Narayana, S.V.L. / Babu, Y.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Structure of diisopropyl fluorophosphate-inhibited factor D.
Authors: Cole, L.B. / Chu, N. / Kilpatrick, J.M. / Volanakis, J.E. / Narayana, S.V. / Babu, Y.S.
History
DepositionFeb 18, 1997Processing site: BNL
Revision 1.0Feb 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FACTOR D
B: FACTOR D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2104
Polymers48,8782
Non-polymers3322
Water4,720262
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.600, 125.700, 41.900
Angle α, β, γ (deg.)90.00, 110.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FACTOR D


Mass: 24438.807 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ISOLATED FROM A PATIENT WITH FANCONI'S SYNDROME / Source: (natural) Homo sapiens (human) / References: UniProt: P00746, complement factor D
#2: Chemical ChemComp-DFP / DIISOPROPYL PHOSPHONATE


Mass: 166.155 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15O3P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.05 Å3/Da / Density % sol: 40.11 %
Crystal growpH: 5.8
Details: INHIBITED PROTEIN WAS CRYSTALLIZED FROM 12-16% PEG 6000 AND 0.2 M NACL,50MM MES BUFFER, PH=5.6-5.8.
PH range: 5.6-5.8
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: used to seeding / PH range low: 5.8 / PH range high: 5.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMMES1reservoir
212-16 %PEG60001reservoir
30.2 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS X1000 / Detector: CCD / Date: Feb 1, 1995
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→15 Å / Num. obs: 14663 / % possible obs: 95.4 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.053 / Rsym value: 0.082 / Net I/σ(I): 23.2
Reflection shellResolution: 2.4→2.55 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 4.6 / Rsym value: 0.17 / % possible all: 75
Reflection
*PLUS
Num. measured all: 64840

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Processing

Software
NameVersionClassification
XENGENdata collection
XENGENdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DSU

1dsu


Resolution: 2.4→8 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 100000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: FINAL STAGES / σ(F): 2 / Details: DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1402 10 %RANDOM
Rwork0.148 ---
obs0.148 13754 92 %-
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3424 0 20 262 3706
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shellResolution: 2.4→2.51 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.272 104 5.6 %
Rwork0.216 975 -
obs--58.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2TOPH19.PEP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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