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- PDB-5z2r: ThDP-Mn2+ complex of R395K variant of EcMenD soaked with 2-ketogl... -

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Basic information

Entry
Database: PDB / ID: 5z2r
TitleThDP-Mn2+ complex of R395K variant of EcMenD soaked with 2-ketoglutarate for 5 min
Components2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
KeywordsTRANSFERASE / complex
Function / homology
Function and homology information


2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase / 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity / menaquinone biosynthetic process / thiamine pyrophosphate binding / manganese ion binding / magnesium ion binding / protein homodimerization activity
Similarity search - Function
Menaquinone biosynthesis protein MenD, middle domain / Middle domain of thiamine pyrophosphate / 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / TPP-binding domain / Thiamin diphosphate-binding fold ...Menaquinone biosynthesis protein MenD, middle domain / Middle domain of thiamine pyrophosphate / 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / TPP-binding domain / Thiamin diphosphate-binding fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / : / Chem-TD6 / THIAMINE DIPHOSPHATE / 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsQin, M.M. / Guo, Z.H.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
Hong Kong
CitationJournal: Biochem. J. / Year: 2018
Title: Two active site arginines are critical determinants of substrate binding and catalysis in MenD: a thiamine-dependent enzyme in menaquinone biosynthesis.
Authors: Qin, M.M. / Song, H.G. / Dai, X. / Chen, Y.Z. / Guo, Z.H.
History
DepositionJan 3, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 2.0Aug 18, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / 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_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _struct_conn.pdbx_dist_value / _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_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
B: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
C: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
D: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
E: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
F: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
G: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
H: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)497,10755
Polymers491,2468
Non-polymers5,86147
Water57,4683190
1
A: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
B: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
C: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
D: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,61228
Polymers245,6234
Non-polymers2,98924
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24500 Å2
ΔGint-112 kcal/mol
Surface area66770 Å2
MethodPISA
2
E: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
F: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
G: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
H: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,49527
Polymers245,6234
Non-polymers2,87223
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25600 Å2
ΔGint-135 kcal/mol
Surface area67080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.630, 90.750, 172.370
Angle α, β, γ (deg.)82.910, 75.710, 64.200
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(CHAIN A AND (RESSEQ 3:23 OR RESSEQ 25:53 OR (RESID...
21(CHAIN B AND (RESSEQ 3:23 OR RESSEQ 25:42 OR (RESID...
31(CHAIN C AND (RESSEQ 3:23 OR RESSEQ 25:42 OR (RESID...
41(CHAIN D AND (RESSEQ 3:23 OR RESSEQ 25:42 OR (RESID...
51(CHAIN E AND (RESSEQ 3:23 OR RESSEQ 25:42 OR (RESID...
61(CHAIN F AND (RESSEQ 3:23 OR RESSEQ 25:42 OR (RESID...
71(CHAIN G AND (RESSEQ 3:23 OR RESSEQ 25:42 OR (RESID...
81(CHAIN H AND (RESSEQ 3:23 OR RESSEQ 25:42 OR (RESID...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(CHAIN A AND (RESSEQ 3:23 OR RESSEQ 25:53 OR (RESID...A3 - 23
121(CHAIN A AND (RESSEQ 3:23 OR RESSEQ 25:53 OR (RESID...A25 - 53
131(CHAIN A AND (RESSEQ 3:23 OR RESSEQ 25:53 OR (RESID...A54
141(CHAIN A AND (RESSEQ 3:23 OR RESSEQ 25:53 OR (RESID...A1 - 556
151(CHAIN A AND (RESSEQ 3:23 OR RESSEQ 25:53 OR (RESID...A1 - 556
161(CHAIN A AND (RESSEQ 3:23 OR RESSEQ 25:53 OR (RESID...A1 - 556
171(CHAIN A AND (RESSEQ 3:23 OR RESSEQ 25:53 OR (RESID...A1 - 556
181(CHAIN A AND (RESSEQ 3:23 OR RESSEQ 25:53 OR (RESID...A1 - 556
191(CHAIN A AND (RESSEQ 3:23 OR RESSEQ 25:53 OR (RESID...A1 - 556
211(CHAIN B AND (RESSEQ 3:23 OR RESSEQ 25:42 OR (RESID...B3 - 23
221(CHAIN B AND (RESSEQ 3:23 OR RESSEQ 25:42 OR (RESID...B25 - 42
231(CHAIN B AND (RESSEQ 3:23 OR RESSEQ 25:42 OR (RESID...B43
241(CHAIN B AND (RESSEQ 3:23 OR RESSEQ 25:42 OR (RESID...B1 - 556
251(CHAIN B AND (RESSEQ 3:23 OR RESSEQ 25:42 OR (RESID...B1 - 556
261(CHAIN B AND (RESSEQ 3:23 OR RESSEQ 25:42 OR (RESID...B1 - 556
271(CHAIN B AND (RESSEQ 3:23 OR RESSEQ 25:42 OR (RESID...B1 - 556
311(CHAIN C AND (RESSEQ 3:23 OR RESSEQ 25:42 OR (RESID...C3 - 23
321(CHAIN C AND (RESSEQ 3:23 OR RESSEQ 25:42 OR (RESID...C25 - 42
331(CHAIN C AND (RESSEQ 3:23 OR RESSEQ 25:42 OR (RESID...C43
341(CHAIN C AND (RESSEQ 3:23 OR RESSEQ 25:42 OR (RESID...C1 - 556
351(CHAIN C AND (RESSEQ 3:23 OR RESSEQ 25:42 OR (RESID...C1 - 556
361(CHAIN C AND (RESSEQ 3:23 OR RESSEQ 25:42 OR (RESID...C1 - 556
371(CHAIN C AND (RESSEQ 3:23 OR RESSEQ 25:42 OR (RESID...C1 - 556
411(CHAIN D AND (RESSEQ 3:23 OR RESSEQ 25:42 OR (RESID...D0
511(CHAIN E AND (RESSEQ 3:23 OR RESSEQ 25:42 OR (RESID...E3 - 23
521(CHAIN E AND (RESSEQ 3:23 OR RESSEQ 25:42 OR (RESID...E25 - 42
531(CHAIN E AND (RESSEQ 3:23 OR RESSEQ 25:42 OR (RESID...E43
541(CHAIN E AND (RESSEQ 3:23 OR RESSEQ 25:42 OR (RESID...E1 - 556
551(CHAIN E AND (RESSEQ 3:23 OR RESSEQ 25:42 OR (RESID...E1 - 556
561(CHAIN E AND (RESSEQ 3:23 OR RESSEQ 25:42 OR (RESID...E1 - 556
571(CHAIN E AND (RESSEQ 3:23 OR RESSEQ 25:42 OR (RESID...E1 - 556
611(CHAIN F AND (RESSEQ 3:23 OR RESSEQ 25:42 OR (RESID...F0
711(CHAIN G AND (RESSEQ 3:23 OR RESSEQ 25:42 OR (RESID...G0
811(CHAIN H AND (RESSEQ 3:23 OR RESSEQ 25:42 OR (RESID...H3 - 23
821(CHAIN H AND (RESSEQ 3:23 OR RESSEQ 25:42 OR (RESID...H25 - 42
831(CHAIN H AND (RESSEQ 3:23 OR RESSEQ 25:42 OR (RESID...H43
841(CHAIN H AND (RESSEQ 3:23 OR RESSEQ 25:42 OR (RESID...H1 - 556
851(CHAIN H AND (RESSEQ 3:23 OR RESSEQ 25:42 OR (RESID...H1 - 556
861(CHAIN H AND (RESSEQ 3:23 OR RESSEQ 25:42 OR (RESID...H1 - 556
871(CHAIN H AND (RESSEQ 3:23 OR RESSEQ 25:42 OR (RESID...H1 - 556

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / SEPHCHC synthase / Menaquinone biosynthesis protein MenD


Mass: 61405.766 Da / Num. of mol.: 8 / Mutation: R395K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: menD, b2264, JW5374 / Production host: Escherichia coli (E. coli)
References: UniProt: P17109, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase

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Non-polymers , 7 types, 3237 molecules

#2: Chemical
ChemComp-TD6 / (4S)-4-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3lambda~5~-thiazol-2-yl}-4-hydroxybutanoic acid


Mass: 527.403 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C16H25N4O10P2S
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#4: Chemical...
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


Mass: 425.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#7: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3190 / Source method: isolated from a natural source / Formula: H2O

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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: 2.52 Å3/Da / Density % sol: 51.14 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M Ammonium acetate, 0.1M Tris pH 7.5, 12% w/v Polyethylene glycol 10000, 0.06M Magnesium formate, 3% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→40.46 Å / Num. obs: 187417 / % possible obs: 88 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 9.2
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.108 / % possible all: 77.1

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.22data extraction
Aimlessdata scaling
PHENIXphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EJ8

5ej8


Resolution: 2.3→38.63 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 19.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.201 1995 1.06 %
Rwork0.17 185390 -
obs0.171 187385 88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.68 Å2 / Biso mean: 22.56 Å2 / Biso min: 1 Å2
Refinement stepCycle: final / Resolution: 2.3→38.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34130 0 364 3190 37684
Biso mean--26.28 28.83 -
Num. residues----4447
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A19509X-RAY DIFFRACTIONPOSITIONAL0
12B19509X-RAY DIFFRACTIONPOSITIONAL0
13C19509X-RAY DIFFRACTIONPOSITIONAL0
14D19509X-RAY DIFFRACTIONPOSITIONAL0
15E19509X-RAY DIFFRACTIONPOSITIONAL0
16F19509X-RAY DIFFRACTIONPOSITIONAL0
17G19509X-RAY DIFFRACTIONPOSITIONAL0
18H19509X-RAY DIFFRACTIONPOSITIONAL0
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.35750.26061320.1988116571178978
2.3575-2.42120.19631120.1919119201203279
2.4212-2.49250.23571320.1816121791231181
2.4925-2.57290.25191340.1813122501238482
2.5729-2.66480.21581410.1845124111255282
2.6648-2.77150.22081120.1889122401235282
2.7715-2.89760.18861270.1913111091123674
2.8976-3.05030.23651470.1863128711301886
3.0503-3.24130.23311520.181148051495798
3.2413-3.49150.20111650.1724147361490198
3.4915-3.84250.17731580.1575148031496198
3.8425-4.39790.17671570.1455148021495999
4.3979-5.53830.17261690.1452148161498599
5.5383-38.6380.17781570.1689147911494898
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)
10.0290.03130.00880.03080.01380.0357-0.0127-0.0518-0.04430.0646-0.00840.0894-0.0011-0.0666-0.02360.1111-0.05840.03660.0456-0.00460.1456-47.1154-12.716913.482
20.0014-0.0011-0.00030.0008-0.00010.00050.0045-0.0013-0.0022-0.0153-0.00950.00450.017-0.0022-0.00010.154-0.0187-0.02520.103-0.00770.1324-35.5738-23.6168-10.0752
30.0048-0.00910.02040.065-0.02330.07380.00530.02010.0051-0.0084-0.0371-0.00160.09260.0496-0.00590.15-0.00680.00410.06870.00470.108-13.6927-32.62-0.7474
40.00870.0044-0.00340.01350.00640.0064-0.0202-0.0001-0.02450.04090.0114-0.03520.03960.0281-00.179-0.00540.00920.07040.02630.1405-16.4205-35.8420.7849
50.0179-0.03250.01510.0553-0.02080.0434-0.0596-0.0369-0.00390.07070.0147-0.04690.02680.0541-0.02380.2228-0.028-0.00310.04270.01930.116-21.772-25.881628.1668
60.0127-0.0087-0.00650.00640.00020.01060.0074-0.0172-0.00310.08840.0012-0.0470.01910.02630.00660.2350.0133-0.0050.10860.0360.134-13.0008-34.440226.5795
7-0.00010.00410.00570.03530.01180.01620.0205-0.03370.010.03390.0123-0.0239-0.0190.02030.05610.1354-0.087-0.0126-0.0514-0.00660.0979-16.47770.094719.2902
80.0126-0.0010.00170.0026-0.00290.00920.0053-0.038-0.02840.0331-0.0014-0.0514-0.0106-0.01990.00250.1974-0.0903-0.0340.1617-0.01050.2672-5.227412.734117.9921
90.0150.0009-0.00470.0074-0.00240.0101-0.0151-0.03180.02720.10870.04490.0491-0.0575-0.05430.00810.33720.02660.07240.1540.00130.1612-47.094418.801738.1652
100.00120.0002-0.00260.0099-0.00750.0084-0.0109-0.02220.00290.06120.01380.0289-0.04870.012300.24470.00470.05460.11540.00260.1567-44.616521.994231.574
110.0109-0.0031-0.0090.06220.00660.051-0.0196-0.0251-0.00510.14030.05570.01160.0033-0.04850.02780.27910.00670.04610.14320.00990.1148-38.8484-2.891643.1927
120.03470.00250.01220.04520.04080.04440.0519-0.070.00340.09870.01860.02470.063-0.0230.01270.3318-0.00820.05190.18420.04520.1481-39.8621-11.657446.8789
130.0175-0.0070.01060.0868-0.02440.02020.02930.034-0.0029-0.0309-0.0373-0.0221-0.00690.0291-0.03210.0918-0.01890.00490.05960.00140.0838-19.24870.0646-12.2393
140.00220.00150.00070.00080.0005-0.0002-0.00550.0103-0.00960.008-0.0186-0.00260.0073-0.01200.2483-0.0443-0.00420.1647-0.02730.2146-41.5199-24.8563-11.6104
150.0268-0.0053-0.00230.0239-0.00950.01870.02630.0185-0.0013-0.0454-0.05040.06920.0376-0.0712-0.02530.0815-0.0304-0.020.1041-0.02290.1377-56.9671-14.5783-19.8788
160.0270.0139-0.0210.0066-0.01030.01620.03820.03830.0133-0.00120.02030.0253-0.0253-0.02880.00370.12250.0498-0.03050.1887-0.02480.1187-54.24453.9438-32.7804
170.01120.00310.00920.0306-0.01240.01590.00090.0525-0.0006-0.03230.01430.0404-0.0844-0.05530.0050.1450.0413-0.01520.10040.00460.0752-44.376313.5164-28.9191
180.0032-0.00010.00030.0012-0.00080.00040.01380.01320.0133-0.00650.00310.0012-0.0025-0.007300.23240.0657-0.00630.27840.00560.2763-67.14988.7971-25.576
190.0142-0.0094-0.01880.02980.0210.03270.03240.0186-0.02620.01790.00140.0163-0.0798-0.03570.0250.1177-0.00540.01690.02560.00570.0813-45.950716.13880.8745
200.0041-0.0036-0.00340.00270.00370.0040.0040.02260.02140.0121-0.0144-0.0125-0.0219-0.043600.18950.02060.05510.12440.00040.1918-56.880421.50714.0179
210.01840.01720.01860.0170.01740.02140.017-0.02490.03580.0811-0.0106-0.0735-0.02960.01660.01370.1968-0.14740.0276-0.0519-0.02010.1813-10.744233.40127.7455
220.004-0.0041-0.0030.03280.02230.01760.01710.01050.025-0.06710.0025-0.0496-0.06190.0230.01150.2043-0.05810.0654-0.00020.02860.1222-24.214833.1072-14.2722
230.01510.0088-0.00920.00980.00270.01590.00390.0022-0.0248-0.0344-0.026-0.0642-0.0310.00110.00080.2337-0.02290.01480.15290.06350.1723-23.686728.2257-26.1886
240.00270.00150.00780.00870.01280.03550.0020.006-0.0001-0.04570.0143-0.0032-0.04120.04610.0060.2636-0.01890.06540.13280.02730.2203-15.791934.609-19.9034
250.004-0.0024-0.00150.01890.03310.0864-0.02340.0120.03810.04550.0045-0.05280.06050.0171-0.0232-0.00360.0063-0.02770.1018-0.02030.09-14.4394-8.6082-57.0972
260.006-0.00810.00160.01370.0020.00960.0092-0.01680.01510.05430.01110.0018-0.0716-0.02530.00040.1190.0197-0.00920.149-0.02850.1375-24.72144.4059-55.3083
270.0218-0.00610.01990.01380.0060.0314-0.0032-0.0147-0.05680.0008-0.01850.02030.0813-0.0726-0.00350.0863-0.02120.01390.11820.00160.1543-45.1399-33.2461-49.577
280.01910.00850.00460.0052-0.00030.00380.0316-0.0234-0.030.03710.05310.00730.0178-0.00910.00270.22280.02130.01960.1020.01410.181-27.0265-40.5137-36.241
290.0155-0.0112-0.00330.0282-0.02480.02940.0272-0.0234-0.0550.0038-0.0008-0.00740.05550.04490.00090.10520.0159-0.00730.11280.00410.0745-14.8756-34.5124-39.929
300.00080.00140.00080.0039-0.00010.0009-0.02120.0106-0.0257-0.0097-0.02370.00160.02230.006100.285-0.0019-0.01320.095-0.01060.2332-27.64-52.8709-43.1677
310.0298-0.0165-0.01830.041-0.01970.03960.01730.0297-0.0008-0.01460.00640.00550.05780.07210.05370.07950.0232-0.00640.1322-0.01850.0847-12.4462-37.1802-69.891
320.002100.00050.00770.0015-0.0001-0.00840.03-0.0328-0.0208-0.01440.00870.02770.038400.21620.027-0.02430.1701-0.04480.1726-9.8188-45.8294-83.9575
330.0188-0.0010.00210.01520.00540.0034-0.01780.0440.0664-0.00560.0208-0.0087-0.01430.0434-0.00310.02-0.0006-0.0010.2758-0.02060.191618.5022-12.4594-75.6565
340.02940.00270.00980.02950.04450.07190.0262-0.00830.04110.04540.0213-0.05380.07240.09020.05630.01860.0349-0.05780.2313-0.05290.151214.4575-21.5347-61.6369
350.01050.00860.00220.00870.00980.0205-0.0292-0.05340.0470.0039-0.0019-0.0114-0.00850.05-0.00250.12310.0306-0.04310.21390.0040.14477.9926-21.7989-42.8999
360.03560.0057-0.00740.01170.00730.0120.0135-0.05020.02990.01380.0324-0.01590.00060.03130.03540.08170.0197-0.06840.2399-0.04380.192517.2979-18.4582-49.0652
370.0226-0.0098-0.01160.0117-0.00980.04530.0060.0266-0.0684-0.0043-0.00320.04430.0343-0.0181-0.0070.0611-0.0071-0.01060.1384-0.01940.1193-37.9977-25.0366-83.4326
38-0.0002-0.0008-0.00120.00270.00020.0038-0.00580.0128-0.05840.0159-0.00370.0260.0238-0.0235-00.0871-0.0160.01480.1939-0.02310.1758-47.5776-22.1642-65.3736
390.0384-0.0060.02620.0299-0.02290.03140.0156-0.0042-0.0120.0309-0.04110.0045-0.094-0.085-0.03990.06830.0421-0.00190.1418-0.00560.1069-42.179712.9444-67.8383
400.0072-0.0018-0.0030.02750.02880.02780.02120.0226-0.0163-0.06320.0030.0018-0.0541-0.05250.00730.08380.0332-0.00320.20080.00910.1193-44.48624.7081-91.985
410.00380.0029-0.00440.0215-0.01950.01640.01870.05290.0656-0.0437-0.025-0.0579-0.043-0.010100.1960.0655-0.02350.2190.01590.1993-36.98468.0392-102.1607
420.0085-0.0067-0.00320.0063-0.00280.00880.0030.0535-0.0056-0.0294-0.03690.0242-0.0122-0.02200.15570.0408-0.0310.23040.02040.1154-41.855715.2103-94.7057
430.03580.0167-0.00990.0048-0.00320.00420.00490.06190.0502-0.0511-0.0193-0.0444-0.0242-0.0298-0.0589-0.10.01910.03290.16270.02270.0687-14.1315-3.6192-88.1994
440.01430.0056-0.00110.0177-0.00230.0004-0.00230.03020.0325-0.0127-0.0131-0.0032-0.01030.0314-0.01190.052-0.0290.03080.23780.04170.18682.43543.2222-86.4537
450.0009-0.00010.00010.0020.00070.0007-0.0080.0070.00640.0044-0.0125-0.0102-0.01710.01700.27140.0353-0.03530.2959-0.02820.28133.3049-33.1453-94.1377
460.0229-0.0050.01010.01310.00480.03090.08420.1109-0.0316-0.0692-0.0603-0.01780.09590.07330.00580.22160.0888-0.0040.2636-0.0310.1294-9.8196-38.5514-104.9304
470.0474-0.02960.01420.02060.00470.03790.08610.1086-0.0358-0.0683-0.07270.02760.01840.02940.01420.15210.0693-0.00110.249-0.02580.0937-23.0986-23.4783-113.5238
480.04710.0010.00120.02010.01570.0230.08240.0912-0.0674-0.1035-0.03710.0580.023-0.08320.00540.24460.0643-0.0550.3229-0.01890.1502-35.0463-20.5242-114.0148
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:199)A1 - 199
2X-RAY DIFFRACTION2(CHAIN A AND RESID 200:212)A200 - 212
3X-RAY DIFFRACTION3(CHAIN A AND RESID 213:364)A213 - 364
4X-RAY DIFFRACTION4(CHAIN A AND RESID 365:404)A365 - 404
5X-RAY DIFFRACTION5(CHAIN A AND RESID 405:517)A405 - 517
6X-RAY DIFFRACTION6(CHAIN A AND RESID 518:556)A518 - 556
7X-RAY DIFFRACTION7(CHAIN B AND RESID 1:175)B1 - 175
8X-RAY DIFFRACTION8(CHAIN B AND RESID 176:207)B176 - 207
9X-RAY DIFFRACTION9(CHAIN B AND RESID 208:298)B208 - 298
10X-RAY DIFFRACTION10(CHAIN B AND RESID 299:347)B299 - 347
11X-RAY DIFFRACTION11(CHAIN B AND RESID 348:485)B348 - 485
12X-RAY DIFFRACTION12(CHAIN B AND RESID 486:556)B486 - 556
13X-RAY DIFFRACTION13(CHAIN C AND RESID 1:203)C1 - 203
14X-RAY DIFFRACTION14(CHAIN C AND RESID 204:212)C204 - 212
15X-RAY DIFFRACTION15(CHAIN C AND RESID 213:358)C213 - 358
16X-RAY DIFFRACTION16(CHAIN C AND RESID 359:406)C359 - 406
17X-RAY DIFFRACTION17(CHAIN C AND RESID 407:537)C407 - 537
18X-RAY DIFFRACTION18(CHAIN C AND RESID 538:556)C538 - 556
19X-RAY DIFFRACTION19(CHAIN D AND RESID 1:175)D1 - 175
20X-RAY DIFFRACTION20(CHAIN D AND RESID 176:204)D176 - 204
21X-RAY DIFFRACTION21(CHAIN D AND RESID 205:358)D205 - 358
22X-RAY DIFFRACTION22(CHAIN D AND RESID 359:477)D359 - 477
23X-RAY DIFFRACTION23(CHAIN D AND RESID 478:522)D478 - 522
24X-RAY DIFFRACTION24(CHAIN D AND RESID 523:556)D523 - 556
25X-RAY DIFFRACTION25(CHAIN E AND RESID 1:176)E1 - 176
26X-RAY DIFFRACTION26(CHAIN E AND RESID 177:210)E177 - 210
27X-RAY DIFFRACTION27(CHAIN E AND RESID 211:355)E211 - 355
28X-RAY DIFFRACTION28(CHAIN E AND RESID 356:401)E356 - 401
29X-RAY DIFFRACTION29(CHAIN E AND RESID 402:536)E402 - 536
30X-RAY DIFFRACTION30(CHAIN E AND RESID 537:556)E537 - 556
31X-RAY DIFFRACTION31(CHAIN F AND RESID 1:175)F1 - 175
32X-RAY DIFFRACTION32(CHAIN F AND RESID 176:209)F176 - 209
33X-RAY DIFFRACTION33(CHAIN F AND RESID 210:313)F210 - 313
34X-RAY DIFFRACTION34(CHAIN F AND RESID 314:476)F314 - 476
35X-RAY DIFFRACTION35(CHAIN F AND RESID 477:521)F477 - 521
36X-RAY DIFFRACTION36(CHAIN F AND RESID 522:556)F522 - 556
37X-RAY DIFFRACTION37(CHAIN G AND RESID 1:187)G1 - 187
38X-RAY DIFFRACTION38(CHAIN G AND RESID 188:212)G188 - 212
39X-RAY DIFFRACTION39(CHAIN G AND RESID 213:362)G213 - 362
40X-RAY DIFFRACTION40(CHAIN G AND RESID 363:473)G363 - 473
41X-RAY DIFFRACTION41(CHAIN G AND RESID 474:522)G474 - 522
42X-RAY DIFFRACTION42(CHAIN G AND RESID 523:556)G523 - 556
43X-RAY DIFFRACTION43(CHAIN H AND RESID 1:175)H1 - 175
44X-RAY DIFFRACTION44(CHAIN H AND RESID 176:204)H176 - 204
45X-RAY DIFFRACTION45(CHAIN H AND RESID 205:213)H205 - 213
46X-RAY DIFFRACTION46(CHAIN H AND RESID 214:342)H214 - 342
47X-RAY DIFFRACTION47(CHAIN H AND RESID 343:458)H343 - 458
48X-RAY DIFFRACTION48(CHAIN H AND RESID 459:556)H459 - 556

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