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- PDB-2xwa: Crystal Structure of Complement Factor D Mutant R202A -

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Basic information

Entry
Database: PDB / ID: 2xwa
TitleCrystal Structure of Complement Factor D Mutant R202A
ComponentsCOMPLEMENT FACTOR D
KeywordsHYDROLASE / IMMUNE SYSTEM / SERINE PROTEASE / ALTERNATIVE PATHWAY
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsForneris, F. / Ricklin, D. / Wu, J. / Tzekou, A. / Wallace, R.S. / Lambris, J.D. / Gros, P.
CitationJournal: Science / Year: 2010
Title: Structures of C3B in Complex with Factors B and D Give Insight Into Complement Convertase Formation.
Authors: Forneris, F. / Ricklin, D. / Wu, J. / Tzekou, A. / Wallace, R.S. / Lambris, J.D. / Gros, P.
History
DepositionNov 1, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Database references / Non-polymer description / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,8904
Polymers48,7052
Non-polymers1842
Water1,15364
1
A: COMPLEMENT FACTOR D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4452
Polymers24,3531
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: COMPLEMENT FACTOR D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4452
Polymers24,3531
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.222, 67.491, 133.588
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B
15A
25B
16A
26B
17A
27B
18A
28B
19A
29B
110A
210B
111A
211B

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEHISHIS1AA1 - 411 - 41
21ILEILEHISHIS1BB1 - 411 - 41
12LYSLYSVALVAL1AA50 - 10550 - 105
22LYSLYSVALVAL1BB50 - 10550 - 105
13PROPROASNASN1AA107 - 155107 - 155
23PROPROASNASN1BB107 - 155107 - 155
14CYSCYSALAALA1AA204 - 228204 - 228
24CYSCYSALAALA1BB204 - 228204 - 228
15CYSCYSGLYGLY6AA42 - 4942 - 49
25CYSCYSGLYGLY6BB42 - 4942 - 49
16ARGARGARGARG6AA106106
26ARGARGARGARG6BB106106
17THRTHRCYSCYS6AA198 - 204198 - 204
27THRTHRCYSCYS6BB198 - 204198 - 204
18THRTHRASNASN1AA158 - 174158 - 174
28THRTHRASNASN1BB158 - 174158 - 174
19ARGARGARGARG6AA156 - 157156 - 157
29ARGARGARGARG6BB156 - 157156 - 157
110ARGARGVALVAL1AA176 - 197176 - 197
210ARGARGVALVAL1BB176 - 197176 - 197
111ARGARGARGARG6AA175175
211ARGARGARGARG6BB175175

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11

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Components

#1: Protein COMPLEMENT FACTOR D / ADIPSIN / C3 CONVERTASE ACTIVATOR / PROPERDIN FACTOR D


Mass: 24352.691 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PUPE.05.05 / Cell line (production host): HEK293-E / Production host: HOMO SAPIENS (human) / References: UniProt: P00746, complement factor D
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ARG 227 TO ALA ENGINEERED RESIDUE IN CHAIN B, ARG 227 TO ALA
Sequence detailsRESIDUE NUMBERING IN COORDINATES FOLLOWS THAT OF THE MATURE PROTEIN. THIS APPLIES TO MUTATION R202A ...RESIDUE NUMBERING IN COORDINATES FOLLOWS THAT OF THE MATURE PROTEIN. THIS APPLIES TO MUTATION R202A IN THE COORDINATES.

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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: 2.05 Å3/Da / Density % sol: 39.5 % / Description: NONE
Crystal growpH: 6 / Details: pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→67.49 Å / Num. obs: 10248 / % possible obs: 98.6 % / Observed criterion σ(I): 3.5 / Redundancy: 3.4 % / Biso Wilson estimate: 49.565 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.5
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 4.7 / % possible all: 94.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DSU

1dsu


Resolution: 2.8→40 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.85 / SU B: 42.762 / SU ML: 0.385 / Cross valid method: THROUGHOUT / ESU R Free: 0.486 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28297 491 4.8 %RANDOM
Rwork0.23757 ---
obs0.23982 9719 98.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.414 Å2
Baniso -1Baniso -2Baniso -3
1--2.15 Å20 Å20 Å2
2---2.33 Å20 Å2
3---4.48 Å2
Refinement stepCycle: LAST / Resolution: 2.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3412 0 12 64 3488
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0213509
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2411.9664783
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2715456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.8722.789147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.11415549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0121535
X-RAY DIFFRACTIONr_chiral_restr0.0790.2539
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212683
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.1731.52267
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.29923626
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.32931242
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.5574.51156
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A300tight positional0.030.05
12B300tight positional0.030.05
21A430tight positional0.030.05
22B430tight positional0.030.05
31A370tight positional0.040.05
32B370tight positional0.040.05
41A193tight positional0.080.05
42B193tight positional0.080.05
81A129tight positional0.030.05
82B129tight positional0.030.05
101A144tight positional0.040.05
102B144tight positional0.040.05
51A53loose positional1.125
52B53loose positional1.125
61A11loose positional0.665
62B11loose positional0.665
71A41loose positional0.615
72B41loose positional0.615
91A22loose positional0.855
92B22loose positional0.855
111A11loose positional0.595
112B11loose positional0.595
11A300tight thermal0.050.5
12B300tight thermal0.050.5
21A430tight thermal0.050.5
22B430tight thermal0.050.5
31A370tight thermal0.050.5
32B370tight thermal0.050.5
41A193tight thermal0.060.5
42B193tight thermal0.060.5
81A129tight thermal0.050.5
82B129tight thermal0.050.5
101A144tight thermal0.070.5
102B144tight thermal0.070.5
51A53loose thermal0.4610
52B53loose thermal0.4610
61A11loose thermal0.810
62B11loose thermal0.810
71A41loose thermal0.9310
72B41loose thermal0.9310
91A22loose thermal0.3610
92B22loose thermal0.3610
111A11loose thermal1.510
112B11loose thermal1.510
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.469 27 -
Rwork0.313 656 -
obs--91.68 %
Refinement TLS params.Method: refined / Origin x: 10.2708 Å / Origin y: 17.1964 Å / Origin z: 33.1011 Å
111213212223313233
T0.0377 Å20.0252 Å20.0044 Å2-0.0424 Å20.0044 Å2--0.1892 Å2
L1.3667 °20.2856 °2-0.1184 °2-1.804 °20.946 °2--1.7626 °2
S0.0265 Å °0.0206 Å °0.1119 Å °0.1605 Å °0.0286 Å °-0.0705 Å °0.116 Å °0.0352 Å °-0.0551 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 228
2X-RAY DIFFRACTION1B1 - 228

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