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- PDB-1dle: FACTOR B SERINE PROTEASE DOMAIN -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1dle
TitleFACTOR B SERINE PROTEASE DOMAIN
ComponentsCOMPLEMENT FACTOR B
KeywordsHYDROLASE / SERINE PROTEASE / COMPLEMENT SYSTEM / FACTOR B / PROTEIN-PROTEIN INTERACTION / ACTIVATION MECHANISM / BETA-BARREL FOLD
Function / homology
Function and homology information


alternative-complement-pathway C3/C5 convertase / classical-complement-pathway C3/C5 convertase complex / complement binding / Alternative complement activation / Activation of C3 and C5 / complement activation, alternative pathway / complement activation / Regulation of Complement cascade / response to bacterium / blood microparticle ...alternative-complement-pathway C3/C5 convertase / classical-complement-pathway C3/C5 convertase complex / complement binding / Alternative complement activation / Activation of C3 and C5 / complement activation, alternative pathway / complement activation / Regulation of Complement cascade / response to bacterium / blood microparticle / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Complement factor B / Complement B/C2 / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/SCR/CCP superfamily / Sushi/CCP/SCR domain profile. / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. ...Complement factor B / Complement B/C2 / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/SCR/CCP superfamily / Sushi/CCP/SCR domain profile. / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsJing, H. / Xu, Y. / Carson, M. / Moore, D. / Macon, K.J. / Volanakis, J.E. / Narayana, S.V.
CitationJournal: EMBO J. / Year: 2000
Title: New structural motifs on the chymotrypsin fold and their potential roles in complement factor B.
Authors: Jing, H. / Xu, Y. / Carson, M. / Moore, D. / Macon, K.J. / Volanakis, J.E. / Narayana, S.V.
History
DepositionDec 9, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Nov 13, 2019Group: Database references / Structure summary / Category: struct_keywords / struct_ref_seq_dif / Item: _struct_keywords.text / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COMPLEMENT FACTOR B
B: COMPLEMENT FACTOR B


Theoretical massNumber of molelcules
Total (without water)67,3972
Polymers67,3972
Non-polymers00
Water9,314517
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-9 kcal/mol
Surface area25000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.643, 74.259, 73.258
Angle α, β, γ (deg.)90.00, 95.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein COMPLEMENT FACTOR B /


Mass: 33698.562 Da / Num. of mol.: 2 / Fragment: SERINE PROTEASE DOMAIN / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: BLOOD / Tissue fraction: SERUM / References: UniProt: P00751
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 517 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG-1000, MES, TRIS, SODIUM CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5
Details: drop consists of equal amounts of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
220 mMTris-HCl1drop
3100 mM1dropNaCl
435 %PEG10001reservoir
530 mMMES1reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 22, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 32252 / Num. obs: 32252 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 19
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.315 / % possible all: 94.1
Reflection shell
*PLUS
% possible obs: 94.1 %

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Processing

Software
NameClassification
CNSrefinement
SCALEPACKdata scaling
AMoREphasing
XTALVIEWrefinement
MLPHAREphasing
DMMultimodel building
DENZOdata reduction
DMMultiphasing
RefinementResolution: 2.1→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.249 3214 -RANDOM
Rwork0.209 ---
all0.21 32125 --
obs0.21 32125 99 %-
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4508 0 0 517 5025
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d1.43
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.43

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