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- PDB-5fcr: MOUSE COMPLEMENT FACTOR D -

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Basic information

Entry
Database: PDB / ID: 5fcr
TitleMOUSE COMPLEMENT FACTOR D
ComponentsComplement factor DFactor D
KeywordsHYDROLASE
Function / homology
Function and homology information


Alternative complement activation / complement factor D / Platelet degranulation / complement activation, alternative pathway / Notch signaling pathway / Neutrophil degranulation / response to bacterium / endopeptidase activity / serine-type endopeptidase activity / extracellular space
Similarity search - Function
Complement factor D / 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 ...Complement factor D / 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
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsMac Sweeney, A.
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: Small-molecule factor D inhibitors targeting the alternative complement pathway.
Authors: Maibaum, J. / Liao, S.M. / Vulpetti, A. / Ostermann, N. / Randl, S. / Rudisser, S. / Lorthiois, E. / Erbel, P. / Kinzel, B. / Kolb, F.A. / Barbieri, S. / Wagner, J. / Durand, C. / Fettis, K. ...Authors: Maibaum, J. / Liao, S.M. / Vulpetti, A. / Ostermann, N. / Randl, S. / Rudisser, S. / Lorthiois, E. / Erbel, P. / Kinzel, B. / Kolb, F.A. / Barbieri, S. / Wagner, J. / Durand, C. / Fettis, K. / Dussauge, S. / Hughes, N. / Delgado, O. / Hommel, U. / Gould, T. / Mac Sweeney, A. / Gerhartz, B. / Cumin, F. / Flohr, S. / Schubart, A. / Jaffee, B. / Harrison, R. / Risitano, A.M. / Eder, J. / Anderson, K.
History
DepositionDec 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Nov 23, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Complement factor D
B: Complement factor D
C: Complement factor D
D: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,76810
Polymers101,9474
Non-polymers8216
Water15,133840
1
A: Complement factor D


Theoretical massNumber of molelcules
Total (without water)25,4871
Polymers25,4871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8173
Polymers25,4871
Non-polymers3302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8213
Polymers25,4871
Non-polymers3342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6433
Polymers25,4871
Non-polymers1562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.271, 52.866, 84.278
Angle α, β, γ (deg.)90.46, 98.04, 90.14
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYAA16 - 2441 - 230
21GLYGLYBB16 - 2441 - 230
12THRTHRAA16 - 2421 - 228
22THRTHRCC16 - 2421 - 228
13GLYGLYAA16 - 2441 - 230
23GLYGLYDD16 - 2441 - 230
14THRTHRBB16 - 2421 - 228
24THRTHRCC16 - 2421 - 228
15GLYGLYBB16 - 2441 - 230
25GLYGLYDD16 - 2441 - 230
16THRTHRCC16 - 2421 - 228
26THRTHRDD16 - 2421 - 228

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Complement factor D / Factor D / 28 kDa adipocyte protein / Adipsin / C3 convertase activator / Properdin factor D


Mass: 25486.682 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cfd, Adn, Df / Production host: Escherichia coli (E. coli) / References: UniProt: P03953, complement factor D

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Non-polymers , 5 types, 846 molecules

#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#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: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 840 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Mouse FD was crystallized by the sitting drop vapour diffusion method. A 1 uL FD solution (14.4 mg/mL FD, 50 mM Tris pH 8.0, 100 mM NaCl) was mixed with 1 uL reservoir solution (0.1 M HEPES ...Details: Mouse FD was crystallized by the sitting drop vapour diffusion method. A 1 uL FD solution (14.4 mg/mL FD, 50 mM Tris pH 8.0, 100 mM NaCl) was mixed with 1 uL reservoir solution (0.1 M HEPES pH 7.0, 30% v/v Jeffamine ED-2001 pH 7.0) and equilibrated against 200 uL reservoir solution.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.25→88.35 Å / Num. obs: 215515 / % possible obs: 88.3 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 13.9
Reflection shellResolution: 1.25→1.28 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.72 / % possible all: 75.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FCK

5fck


Resolution: 1.25→83.45 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.308 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19599 10776 5 %RANDOM
Rwork0.14979 ---
obs0.15209 204735 88.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.735 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.31 Å2-0 Å2
2---0.14 Å2-0.08 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.25→83.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6947 0 49 840 7836
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0197375
X-RAY DIFFRACTIONr_bond_other_d0.0180.026815
X-RAY DIFFRACTIONr_angle_refined_deg2.71.94810120
X-RAY DIFFRACTIONr_angle_other_deg2.304315711
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.375987
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49423.491318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.587151140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1451558
X-RAY DIFFRACTIONr_chiral_restr0.1850.21136
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0218527
X-RAY DIFFRACTIONr_gen_planes_other0.0110.021681
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.431.453762
X-RAY DIFFRACTIONr_mcbond_other4.4271.4493761
X-RAY DIFFRACTIONr_mcangle_it5.4482.1964721
X-RAY DIFFRACTIONr_mcangle_other5.4482.1964722
X-RAY DIFFRACTIONr_scbond_it71.9213613
X-RAY DIFFRACTIONr_scbond_other6.9961.9183609
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.622.7025364
X-RAY DIFFRACTIONr_long_range_B_refined7.87713.9878874
X-RAY DIFFRACTIONr_long_range_B_other7.87713.9878875
X-RAY DIFFRACTIONr_rigid_bond_restr6.679314190
X-RAY DIFFRACTIONr_sphericity_free33.9925216
X-RAY DIFFRACTIONr_sphericity_bonded21.176514604
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A266160.1
12B266160.1
21A270900.07
22C270900.07
31A268020.09
32D268020.09
41B263460.1
42C263460.1
51B267960.08
52D267960.08
61C267300.09
62D267300.09
LS refinement shellResolution: 1.247→1.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 568 -
Rwork0.278 10792 -
obs--62.94 %

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