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- PDB-1fdp: PROENZYME OF HUMAN COMPLEMENT FACTOR D, RECOMBINANT PROFACTOR D -

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Basic information

Entry
Database: PDB / ID: 1fdp
TitlePROENZYME OF HUMAN COMPLEMENT FACTOR D, RECOMBINANT PROFACTOR D
ComponentsPROENZYME OF COMPLEMENT FACTOR D
KeywordsHYDROLASE / SERINE PROTEASE / COMPLEMENT / FACTOR D / PROFACTOR D / ZYMOGEN / PROENZYME
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 / protein maturation / response to bacterium / Platelet degranulation / secretory granule lumen ...complement factor D / Alternative complement activation / complement activation / complement activation, alternative pathway / serine-type peptidase activity / platelet alpha granule lumen / protein maturation / response to bacterium / Platelet degranulation / secretory granule lumen / ficolin-1-rich granule lumen / serine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / 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 / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / 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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJing, H. / Macon, K.J. / Moore, D. / Delucas, L.J. / Volanakis, J.E. / Narayana, S.V.L.
Citation
Journal: Embo J. / Year: 1999
Title: Structural basis of profactor D activation: from a highly flexible zymogen to a novel self-inhibited serine protease, complement factor D.
Authors: Jing, H. / Macon, K.J. / Moore, D. / DeLucas, L.J. / Volanakis, J.E. / Narayana, S.V.
#1: Journal: J.Mol.Biol. / Year: 1998
Title: Structures of Native and Complexed Complement Factor D: Implications of the Atypical His57 Conformation and Self-Inhibitory Loop in the Regulation of Specific Serine Protease Activity
Authors: Jing, H. / Babu, Y.S. / Moore, D. / Kilpatrick, J.M. / Liu, X.-Y. / Volanakis, J.E. / Narayana, S.V.L.
#2: Journal: Protein Sci. / Year: 1996
Title: Complement Factor D, a Novel Serine Protease
Authors: Volanakis, J.E. / Narayana, S.V.L.
#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.L. / 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: 1994
Title: Preliminary Crystallographic Studies on Human Complement Profactor D
Authors: Narayana, S.V.L. / Yamauchi, Y. / Macon, K.J. / Moore, D. / Delucas, L.J. / Volanakis, J.E.
History
DepositionDec 3, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 3, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 7, 2011Group: Database references
Revision 1.4Aug 9, 2023Group: 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROENZYME OF COMPLEMENT FACTOR D
B: PROENZYME OF COMPLEMENT FACTOR D
C: PROENZYME OF COMPLEMENT FACTOR D
D: PROENZYME OF COMPLEMENT FACTOR D


Theoretical massNumber of molelcules
Total (without water)100,5874
Polymers100,5874
Non-polymers00
Water11,367631
1
A: PROENZYME OF COMPLEMENT FACTOR D


Theoretical massNumber of molelcules
Total (without water)25,1471
Polymers25,1471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROENZYME OF COMPLEMENT FACTOR D


Theoretical massNumber of molelcules
Total (without water)25,1471
Polymers25,1471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PROENZYME OF COMPLEMENT FACTOR D


Theoretical massNumber of molelcules
Total (without water)25,1471
Polymers25,1471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: PROENZYME OF COMPLEMENT FACTOR D


Theoretical massNumber of molelcules
Total (without water)25,1471
Polymers25,1471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.050, 70.320, 86.300
Angle α, β, γ (deg.)90.00, 101.98, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.99994, -0.001379, 0.010893), (0.003579, 0.978835, -0.204619), (-0.01038, 0.204646, 0.978781)-8.534, 1.335, 43.1231
2given(-0.999994, -0.000812, -0.003385), (0.000171, -0.982728, 0.185055), (-0.003477, 0.185053, 0.982722)23.146, 32.3961, 28.4763
3given(-0.999827, -0.018451, -0.002494), (0.018433, -0.999804, 0.007156), (-0.002626, 0.007109, 0.999971)32.5385, 33.1221, -13.6664

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Components

#1: Protein
PROENZYME OF COMPLEMENT FACTOR D


Mass: 25146.633 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: ACNPV / Cell (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P00746, complement factor D
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 631 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsCHYMOTRYPSINOGEN NUMBERING IS USED

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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: 1.9 Å3/Da / Density % sol: 36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: CRYSTALLIZATION CONDITIONS: THE RESERVOIR SOLUTION CONTAINED 10-12% PEG-6000 AND 30MM MES (PH5.2). THE DROPS CONTAINED EQUAL VOLUME OF RESERVOIR SOLUTION AND PROTEIN SOLUTION (10MG/ML), ...Details: CRYSTALLIZATION CONDITIONS: THE RESERVOIR SOLUTION CONTAINED 10-12% PEG-6000 AND 30MM MES (PH5.2). THE DROPS CONTAINED EQUAL VOLUME OF RESERVOIR SOLUTION AND PROTEIN SOLUTION (10MG/ML), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
210 mMTris-HCl1drop
30.1 M1dropNaCl
410-12 %PEG60001reservoir
530 mMMES1reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 1, 1997 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE / Protocol: 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. obs: 43713 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 3.9 / % possible all: 96.8
Reflection
*PLUS
Num. measured all: 93825
Reflection shell
*PLUS
% possible obs: 96.8 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CORE REGION OF FACTOR D (1DSU MOLECULE B)

1dsu


Resolution: 2.1→30 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT CORRECTION WAS APPLIED
RfactorNum. reflection% reflectionSelection details
Rfree0.251 4399 10 %RANDOM
Rwork0.204 ---
obs0.204 43713 98.5 %-
Displacement parametersBiso mean: 24.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6133 0 0 631 6764
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.43
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.41
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.77
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINED WITH NCS AVERAGE PHASES
LS refinement shellResolution: 2.1→2.2 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.313 533 10 %
Rwork0.279 4587 -
obs--92.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2TOPH19.SOL
X-RAY DIFFRACTION3TOPH19.PEP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.41
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.77

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