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- PDB-1p8j: CRYSTAL STRUCTURE OF THE PROPROTEIN CONVERTASE FURIN -

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Basic information

Entry
Database: PDB / ID: 1p8j
TitleCRYSTAL STRUCTURE OF THE PROPROTEIN CONVERTASE FURIN
Components
  • DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE INHIBITOR
  • Furin precursor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PROHORMONE CONVERTASE / SPC1 / PACE / P-DOMAIN / CHLOROMETHYLKETONE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


: / zymogen inhibition / Assembly of active LPL and LIPC lipase complexes / Formation of the cornified envelope / Elastic fibre formation / trans-Golgi network transport vesicle membrane / NGF processing / Signaling by PDGF / Activation of Matrix Metalloproteinases / Removal of aminoterminal propeptides from gamma-carboxylated proteins ...: / zymogen inhibition / Assembly of active LPL and LIPC lipase complexes / Formation of the cornified envelope / Elastic fibre formation / trans-Golgi network transport vesicle membrane / NGF processing / Signaling by PDGF / Activation of Matrix Metalloproteinases / Removal of aminoterminal propeptides from gamma-carboxylated proteins / : / Pre-NOTCH Processing in Golgi / TGF-beta receptor signaling activates SMADs / Collagen degradation / : / furin / nerve growth factor production / dibasic protein processing / peptide biosynthetic process / Golgi cisterna / negative regulation of transforming growth factor beta1 production / signal peptide processing / negative regulation of low-density lipoprotein particle receptor catabolic process / secretion by cell / nerve growth factor binding / trans-Golgi network transport vesicle / blastocyst formation / zymogen activation / regulation of endopeptidase activity / peptide hormone processing / regulation of protein catabolic process / positive regulation of transforming growth factor beta receptor signaling pathway / regulation of signal transduction / viral life cycle / peptide binding / trans-Golgi network / serine-type endopeptidase inhibitor activity / protein processing / peptidase activity / endopeptidase activity / protease binding / membrane => GO:0016020 / early endosome / endosome membrane / positive regulation of cell migration / membrane raft / endoplasmic reticulum lumen / Golgi membrane / serine-type endopeptidase activity / endoplasmic reticulum membrane / cell surface / endoplasmic reticulum / extracellular region / membrane / metal ion binding / plasma membrane
Similarity search - Function
Peptidase S8, pro-domain / Peptidase S8, pro-domain superfamily / Peptidase S8 pro-domain / Kexin/furin catalytic domain / P domain / Proprotein convertase P-domain / P/Homo B domain profile. / Peptidase S8/S53 domain / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. ...Peptidase S8, pro-domain / Peptidase S8, pro-domain superfamily / Peptidase S8 pro-domain / Kexin/furin catalytic domain / P domain / Proprotein convertase P-domain / P/Homo B domain profile. / Peptidase S8/S53 domain / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Galactose-binding domain-like / Furin-like repeat / Furin-like repeats / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Growth factor receptor cysteine-rich domain superfamily / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE / Furin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsHenrich, S. / Cameron, A. / Bourenkov, G.P. / Kiefersauer, R. / Huber, R. / Lindberg, I. / Bode, W. / Than, M.E.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: The Crystal Structure of the Proprotein Processing Proteinase Furin Explains its Stringent Specificity
Authors: Henrich, S. / Cameron, A. / Bourenkov, G.P. / Kiefersauer, R. / Huber, R. / Lindberg, I. / Bode, W. / Than, M.E.
History
DepositionMay 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 650 HELIX HELIX RECORDS IN THIS FILE WERE PROVIDED BY THE AUTHOR
Remark 700 SHEET SHEET RECORDS IN THIS FILE WERE PROVIDED BY THE AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Furin precursor
B: Furin precursor
C: Furin precursor
D: Furin precursor
E: Furin precursor
F: Furin precursor
G: Furin precursor
H: Furin precursor
J: DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE INHIBITOR
K: DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE INHIBITOR
L: DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE INHIBITOR
M: DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE INHIBITOR
N: DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE INHIBITOR
P: DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE INHIBITOR
Q: DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE INHIBITOR
R: DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)426,623110
Polymers415,20616
Non-polymers11,41694
Water41,5252305
1
A: Furin precursor
B: Furin precursor
C: Furin precursor
D: Furin precursor
J: DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE INHIBITOR
K: DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE INHIBITOR
L: DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE INHIBITOR
M: DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,81555
Polymers207,6038
Non-polymers6,21247
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Furin precursor
F: Furin precursor
G: Furin precursor
H: Furin precursor
N: DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE INHIBITOR
P: DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE INHIBITOR
Q: DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE INHIBITOR
R: DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,80755
Polymers207,6038
Non-polymers5,20447
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Furin precursor
N: DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,16315
Polymers51,9012
Non-polymers1,26213
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-109 kcal/mol
Surface area17600 Å2
MethodPISA
4
C: Furin precursor
L: DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,65311
Polymers51,9012
Non-polymers7539
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-90 kcal/mol
Surface area17600 Å2
MethodPISA
5
A: Furin precursor
J: DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,34618
Polymers51,9012
Non-polymers3,44516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-89 kcal/mol
Surface area19780 Å2
MethodPISA
6
F: Furin precursor
P: DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,38416
Polymers51,9012
Non-polymers1,48314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-108 kcal/mol
Surface area18280 Å2
MethodPISA
7
G: Furin precursor
Q: DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,38612
Polymers51,9012
Non-polymers1,48510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-76 kcal/mol
Surface area17880 Å2
MethodPISA
8
B: Furin precursor
K: DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,87512
Polymers51,9012
Non-polymers97410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-95 kcal/mol
Surface area17600 Å2
MethodPISA
9
H: Furin precursor
R: DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,87512
Polymers51,9012
Non-polymers97410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-84 kcal/mol
Surface area17670 Å2
MethodPISA
10
D: Furin precursor
M: DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,94214
Polymers51,9012
Non-polymers1,04112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-105 kcal/mol
Surface area17570 Å2
MethodPISA
11
A: Furin precursor
J: DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE INHIBITOR
hetero molecules

G: Furin precursor
Q: DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,73230
Polymers103,8024
Non-polymers4,93026
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_666x+1,y+1,z+11
Buried area11180 Å2
ΔGint-166 kcal/mol
Surface area35010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.305, 135.392, 137.806
Angle α, β, γ (deg.)103.56, 98.98, 107.09
Int Tables number1
Space group name H-MP1

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Components

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Protein / Protein/peptide , 2 types, 16 molecules ABCDEFGHJKLMNPQR

#1: Protein
Furin precursor / Paired basic amino acid residue cleaving enzyme / PACE / Dibasic processing enzyme


Mass: 51151.336 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: FURIN OR FUR OR PCSK3 / Plasmid: pcDNA3.1(-)-Myc-His / Organ (production host): Ovary cells / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): DG44 / References: UniProt: P23188, furin
#2: Protein/peptide
DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE INHIBITOR


Type: Peptide-like / Class: Inhibitor / Mass: 749.452 Da / Num. of mol.: 8 / Source method: obtained synthetically
Details: THe peptide (decanoyl-Arg-Val-Lys-Arg-chloromethylketone) was chemically synthesized
References: DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE

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Sugars , 3 types, 8 molecules

#3: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[beta-D-galactopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1990.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2[DGalpb1-4DGlcpNAcb1-4]DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,11,10/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1b_1-5]/1-1-2-3-1-4-1-4-3-1-5/a4-b1_a6-k1_b4-c1_c3-d1_c6-i1_d2-e1_d4-g1_e4-f1_g4-h1_i2-j1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 2391 molecules

#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
#7: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 70 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2305 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHE UNBOUND FORM OF THE INHIBITOR IS DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE. UPON REACTION ...THE UNBOUND FORM OF THE INHIBITOR IS DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE. UPON REACTION WITH PROTEIN IT FORMS TWO COVALENT BONDS: 1) A COVALENT BOND TO SER 368 FORMING A HEMIKETAL AR7 AND 2) A COVALENT BOND TO NE2 OF HIS 194

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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: 3.78 Å3/Da / Density % sol: 67.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1.0M (NH4)2SO4, 0.4M Li2SO4, 0.1M Na3Citrate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
21.0 Mammonium sulfate1reservoir
30.4 M1reservoirLi2SO4
40.1 Msodium citrate1reservoirpH6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 28, 2001 / Details: mirrors
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.6→18.83 Å / Num. all: 182735 / Num. obs: 182735 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 27.4 Å2 / Rsym value: 0.1 / Net I/σ(I): 5.2
Reflection shellResolution: 2.6→2.74 Å / Rsym value: 0.347 / % possible all: 97.2
Reflection
*PLUS
Num. measured all: 382735 / Rmerge(I) obs: 0.1
Reflection shell
*PLUS
% possible obs: 97.2 % / Rmerge(I) obs: 0.347

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CCP4phasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→18.82 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1894579.24 / Data cutoff high rms absF: 1894579.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: waters 1-8: potential third calcium binding-site (identical to the suggest Ca401 binding site in subtilisin Carlsberg, 1CSE) waters 9-14: potential ion binding-site with low B factors
RfactorNum. reflection% reflectionSelection details
Rfree0.219 9564 5.2 %SHELLS
Rwork0.188 ---
all0.188 182735 --
obs0.188 182726 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.8965 Å2 / ksol: 0.326073 e/Å3
Displacement parametersBiso mean: 21.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å21.49 Å23.37 Å2
2---1.67 Å23.13 Å2
3---0.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.6→18.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28984 0 634 2305 31923
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it1.021.5
X-RAY DIFFRACTIONc_mcangle_it1.662
X-RAY DIFFRACTIONc_scbond_it1.712
X-RAY DIFFRACTIONc_scangle_it2.572.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.31 1056 3.5 %
Rwork0.264 29128 -
obs--97.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3MY_ION.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION4CARBOHYDRATE.PARAMMY_ION.TOP
Refinement
*PLUS
Lowest resolution: 18.83 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82
LS refinement shell
*PLUS
Rfactor Rfree: 0.31

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