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- PDB-1xwd: Crystal Structure of Human Follicle Stimulating Hormone Complexed... -

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Basic information

Entry
Database: PDB / ID: 1xwd
TitleCrystal Structure of Human Follicle Stimulating Hormone Complexed with its Receptor
Components
  • Follicle stimulating hormone receptor
  • Follitropin beta chain
  • Glycoprotein hormones alpha chain
KeywordsHormone/Growth Factor / Hormone-receptor complex / Leucine-rich repeats / Cysteine-knot motif / Hormone-Growth Factor COMPLEX
Function / homology
Function and homology information


follicle-stimulating hormone receptor activity / regulation of platelet-derived growth factor receptor signaling pathway / regulation of acetylcholine metabolic process / progesterone biosynthetic process / regulation of protein kinase A signaling / regulation of hormone metabolic process / positive regulation of steroid biosynthetic process / follicle-stimulating hormone activity / follicle-stimulating hormone complex / pituitary gonadotropin complex ...follicle-stimulating hormone receptor activity / regulation of platelet-derived growth factor receptor signaling pathway / regulation of acetylcholine metabolic process / progesterone biosynthetic process / regulation of protein kinase A signaling / regulation of hormone metabolic process / positive regulation of steroid biosynthetic process / follicle-stimulating hormone activity / follicle-stimulating hormone complex / pituitary gonadotropin complex / luteinizing hormone secretion / follicle-stimulating hormone secretion / Thyroxine biosynthesis / Mineralocorticoid biosynthesis / primary ovarian follicle growth / Glycoprotein hormones / Reactions specific to the complex N-glycan synthesis pathway / Hormone ligand-binding receptors / Androgen biosynthesis / follicle-stimulating hormone signaling pathway / female gamete generation / Sertoli cell proliferation / gonad development / intracellular water homeostasis / sperm DNA condensation / negative regulation of organ growth / Sertoli cell development / basement membrane organization / transcytosis / regulation of osteoclast differentiation / cellular response to follicle-stimulating hormone stimulus / regulation of systemic arterial blood pressure / female gonad development / regulation of signaling receptor activity / thyroid hormone generation / positive regulation of bone resorption / G protein-coupled peptide receptor activity / negative regulation of bone resorption / organ growth / positive regulation of intracellular estrogen receptor signaling pathway / regulation of chromosome organization / uterus development / peptide hormone binding / thyroid gland development / hormone-mediated signaling pathway / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transforming growth factor beta receptor signaling pathway / locomotory behavior / female pregnancy / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / hormone activity / Golgi lumen / male gonad development / adenylate cyclase-activating G protein-coupled receptor signaling pathway / neuron projection development / spermatogenesis / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / receptor complex / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endosome / positive regulation of cell migration / G protein-coupled receptor signaling pathway / positive regulation of cell population proliferation / positive regulation of gene expression / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / membrane / plasma membrane / cytoplasm
Similarity search - Function
Follicle stimulating hormone receptor / Gonadotropin hormone receptor, transmembrane domain / Gonadotropin hormone receptor transmembrane region / Gonadotropin, beta subunit, conserved site / Glycoprotein hormones beta chain signature 1. / Glycoprotein hormones beta chain signature 2. / Glycoprotein hormone beta chain homologues. / Glycoprotein hormone alpha chain / Glycoprotein hormone / Glycoprotein hormones alpha chain signature 1. ...Follicle stimulating hormone receptor / Gonadotropin hormone receptor, transmembrane domain / Gonadotropin hormone receptor transmembrane region / Gonadotropin, beta subunit, conserved site / Glycoprotein hormones beta chain signature 1. / Glycoprotein hormones beta chain signature 2. / Glycoprotein hormone beta chain homologues. / Glycoprotein hormone alpha chain / Glycoprotein hormone / Glycoprotein hormones alpha chain signature 1. / Glycoprotein hormones alpha chain signature 2. / Glycoprotein hormones alpha chain family profile. / Glycoprotein hormone alpha chain homologues. / Gonadotropin, beta subunit / Glycoprotein hormone subunit beta / Cystine-knot domain / BspA type Leucine rich repeat region / BspA type Leucine rich repeat region (6 copies) / Glycoprotein hormone receptor family / Leucine rich repeat N-terminal domain / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Cystine-knot cytokine / Alpha-Beta Horseshoe / Leucine-rich repeat domain superfamily / Ribbon / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Glycoprotein hormones alpha chain / Follitropin subunit beta / Follicle-stimulating hormone receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 Å
AuthorsFan, Q.R. / Hendrickson, W.A.
CitationJournal: Nature / Year: 2005
Title: Structure of human follicle-stimulating hormone in complex with its receptor.
Authors: Fan, Q.R. / Hendrickson, W.A.
History
DepositionOct 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
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 / 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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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
Revision 2.1Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Revision 3.0Dec 25, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / pdbx_entry_details ...atom_site / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_validate_chiral / pdbx_validate_close_contact / struct_conn
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_seq_id / _atom_site.label_asym_id / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_validate_chiral.auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycoprotein hormones alpha chain
B: Follitropin beta chain
C: Follicle stimulating hormone receptor
D: Glycoprotein hormones alpha chain
E: Follitropin beta chain
F: Follicle stimulating hormone receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,33417
Polymers102,7086
Non-polymers2,62611
Water90150
1
A: Glycoprotein hormones alpha chain
B: Follitropin beta chain
C: Follicle stimulating hormone receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,95111
Polymers51,3543
Non-polymers1,5978
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Glycoprotein hormones alpha chain
E: Follitropin beta chain
F: Follicle stimulating hormone receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3836
Polymers51,3543
Non-polymers1,0293
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.330, 66.938, 148.629
Angle α, β, γ (deg.)90.00, 99.13, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21F
31C
41F
51C
61F
71C
81F
91C
101F
111C
121F
131C
141F
151C
161F
171C
181F
191C
201F
211C
221F
12A
22D
32A
42D
52A
62D
72A
82D
92A
102D
112A
122D
132A
142D
152A
162D
172A
182D
192A
202D
13B
23E
33B
43E
53B
63E
73B
83E
93B
103E
113B
123E
133B
143E
153B
163E
173B
183E
193B
203E
213B
223E
233B
243E
253B
263E
273B
283E

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111CYSCYSASNASN6CC18 - 272 - 11
211CYSCYSASNASN6FF18 - 272 - 11
321ARGARGPHEPHE1CC28 - 6612 - 50
421ARGARGPHEPHE1FF28 - 6612 - 50
531SERSERGLYGLY6CC67 - 6851 - 52
631SERSERGLYGLY6FF67 - 6851 - 52
741PHEPHEPHEPHE1CC69 - 9153 - 75
841PHEPHEPHEPHE1FF69 - 9153 - 75
951SERSERASNASN6CC92 - 9376 - 77
1051SERSERASNASN6FF92 - 9376 - 77
1161LEULEUVALVAL1CC94 - 16678 - 150
1261LEULEUVALVAL1FF94 - 16678 - 150
1371GLYGLYLEULEU6CC167 - 168151 - 152
1471GLYGLYLEULEU6FF167 - 168151 - 152
1581SERSERHISHIS1CC169 - 215153 - 199
1681SERSERHISHIS1FF169 - 215153 - 199
1791GLYGLYALAALA6CC216 - 217200 - 201
1891GLYGLYALAALA6FF216 - 217200 - 201
19101SERSERLEULEU1CC218 - 244202 - 228
20101SERSERLEULEU1FF218 - 244202 - 228
21111ARGARGTYRTYR6CC245 - 250229 - 234
22111ARGARGTYRTYR6FF245 - 250229 - 234
112ASPASPPROPRO4AA6 - 166 - 16
212ASPASPPROPRO4DD6 - 166 - 16
322PHEPHEALAALA6AA17 - 2317 - 23
422PHEPHEALAALA6DD17 - 2317 - 23
532PROPROMETMET4AA24 - 2924 - 29
632PROPROMETMET4DD24 - 2924 - 29
742GLYGLYPROPRO1AA30 - 4030 - 40
842GLYGLYPROPRO1DD30 - 4030 - 40
952LEULEUVALVAL4AA41 - 5341 - 53
1052LEULEUVALVAL4DD41 - 5341 - 53
1162THRTHRTHRTHR1AA54 - 5854 - 58
1262THRTHRTHRTHR1DD54 - 5854 - 58
1372CYSCYSARGARG4AA59 - 6759 - 67
1472CYSCYSARGARG4DD59 - 6759 - 67
1582VALVALTYRTYR1AA68 - 8968 - 89
1682VALVALTYRTYR1DD68 - 8968 - 89
1792HISHISLYSLYS4AA90 - 9190 - 91
1892HISHISLYSLYS4DD90 - 9190 - 91
19102SERSERSERSER6AA9292
20102SERSERSERSER6DD9292
113CYSCYSGLUGLU4BB3 - 43 - 4
213CYSCYSGLUGLU4EE3 - 43 - 4
323LEULEUILEILE1BB5 - 125 - 12
423LEULEUILEILE1EE5 - 125 - 12
533GLUGLUGLUGLU4BB13 - 1513 - 15
633GLUGLUGLUGLU4EE13 - 1513 - 15
743GLUGLUARGARG1BB16 - 3516 - 35
843GLUGLUARGARG1EE16 - 3516 - 35
953ASPASPLEULEU4BB36 - 3736 - 37
1053ASPASPLEULEU4EE36 - 3736 - 37
1163VALVALPROPRO6BB38 - 4238 - 42
1263VALVALPROPRO6EE38 - 4238 - 42
1373ALAALAILEILE4BB43 - 4743 - 47
1473ALAALAILEILE4EE43 - 4743 - 47
1583GLNGLNGLUGLU1BB48 - 5548 - 55
1683GLNGLNGLUGLU1EE48 - 5548 - 55
1793LEULEUTHRTHR4BB56 - 7556 - 75
1893LEULEUTHRTHR4EE56 - 7556 - 75
19103TYRTYRASPASP1BB76 - 9376 - 93
20103TYRTYRASPASP1EE76 - 9376 - 93
21113CYSCYSLEULEU4BB94 - 9994 - 99
22113CYSCYSLEULEU4EE94 - 9994 - 99
23123GLYGLYPROPRO6BB100 - 101100 - 101
24123GLYGLYPROPRO6EE100 - 101100 - 101
25133SERSERPHEPHE1BB102 - 106102 - 106
26133SERSERPHEPHE1EE102 - 106102 - 106
27143GLYGLYGLYGLY6BB107107
28143GLYGLYGLYGLY6EE107107

NCS ensembles :
ID
1
2
3

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Components

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Protein , 3 types, 6 molecules ADBECF

#1: Protein Glycoprotein hormones alpha chain / Follitropin alpha chain / Follicle-stimulating hormone alpha chain / FSH-alpha / Lutropin alpha ...Follitropin alpha chain / Follicle-stimulating hormone alpha chain / FSH-alpha / Lutropin alpha chain / Luteinizing hormone alpha chain / LSH-alpha / Thyrotropin alpha chain / Thyroid-stimulating hormone alpha chain / TSH-alpha / Choriogonadotropin alpha chain / Chorionic gonadotrophin alpha subunit / CG-alpha


Mass: 10217.769 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CGA / Plasmid: pFastBac Dual / Cell line (production host): High 5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01215
#2: Protein Follitropin beta chain / Follicle-stimulating hormone beta subunit / FSH-beta / FSH-B


Mass: 12500.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FSHB / Plasmid: pFastBac Dual / Cell line (production host): High 5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01225
#3: Protein Follicle stimulating hormone receptor / FSH-R / Follitropin receptor


Mass: 28635.830 Da / Num. of mol.: 2 / Fragment: Extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FSHR / Plasmid: pFastBac Dual / Cell line (production host): High 5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P23945

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Sugars , 3 types, 8 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-Manp]{[(2+?)][]{[(?+2)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#6: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


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 , 2 types, 53 molecules

#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.03 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: PEG 3350, lithium sulfate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 26, 2003
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.9→25 Å / Num. all: 25282 / Num. obs: 25282 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 45.2 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 12.4
Reflection shellResolution: 2.9→3 Å / Redundancy: 3 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 3.4 / Num. unique all: 2494 / Rsym value: 0.388 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FL7

1fl7


Resolution: 2.92→25 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.888 / SU B: 37.017 / SU ML: 0.333 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.419 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1262 5 %RANDOM
Rwork0.2193 ---
all0.2213 25282 --
obs0.2213 25282 98.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 56.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.72 Å20 Å2-1.18 Å2
2---0.37 Å20 Å2
3----2.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.92→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6815 0 166 50 7031
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0217160
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.9769737
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3045856
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.57324.472322
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.924151214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.711538
X-RAY DIFFRACTIONr_chiral_restr0.0890.21120
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025292
X-RAY DIFFRACTIONr_nbd_refined0.2550.22955
X-RAY DIFFRACTIONr_nbtor_refined0.3230.24675
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2214
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.279
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0640.22
X-RAY DIFFRACTIONr_mcbond_it1.94854405
X-RAY DIFFRACTIONr_mcangle_it2.88467023
X-RAY DIFFRACTIONr_scbond_it2.90163004
X-RAY DIFFRACTIONr_scangle_it4.2347.52714
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1C1694tight positional0.370.32
2A285tight positional0.40.32
3B462tight positional0.390.32
2A325medium positional0.570.63
3B297medium positional1.050.63
1C178loose positional2.9410
2A60loose positional0.7410
3B59loose positional1.1110
1C1694tight thermal3.663.16
2A285tight thermal6.643.16
3B462tight thermal10.013.16
2A325medium thermal5.236.32
3B297medium thermal16.026.32
1C178loose thermal16.0499.9
2A60loose thermal4.7999.9
3B59loose thermal9.4199.9
LS refinement shellResolution: 2.92→3.08 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.356 192 -
Rwork0.297 3271 -
obs-3463 93.95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4631-0.22970.41580.89660.09861.87940.03670.0033-0.02420.06440.0248-0.0550.11840.1811-0.0615-0.021-0.0261-0.048-0.0824-0.0136-0.038715.6897-8.826251.2914
21.0599-0.186-0.48991.97141.112.41450.0470.2397-0.01930.1828-0.13880.13070.0829-0.1850.0918-0.16650.00350.0194-0.038-0.0058-0.044819.487-43.355720.0938
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 923 - 92
2X-RAY DIFFRACTION1BB3 - 1073 - 107
3X-RAY DIFFRACTION1CC18 - 2592 - 243
4X-RAY DIFFRACTION2DD6 - 926 - 92
5X-RAY DIFFRACTION2EE3 - 1073 - 107
6X-RAY DIFFRACTION2FF18 - 2502 - 234

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