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- PDB-1dst: MUTANT OF FACTOR D WITH ENHANCED CATALYTIC ACTIVITY -

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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 / complement activation, alternative pathway / 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 / complement activation, alternative pathway / 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 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / 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
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
Revision 1.4Oct 16, 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

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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

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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


Mass: 18.015 Da / Num. of mol.: 61 / 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

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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

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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

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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

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