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- PDB-1nkz: Crystal structure of LH2 B800-850 from Rps. acidophila at 2.0 Ang... -

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Basic information

Entry
Database: PDB / ID: 1nkz
TitleCrystal structure of LH2 B800-850 from Rps. acidophila at 2.0 Angstrom resolution
Components(Light-harvesting protein B-800/850, ...) x 2
KeywordsMEMBRANE PROTEIN / LIGHT HARVESTING COMPLEX II / TRANS-MEMBRANE HELICES / RHODOPIN GLUCOSIDE / BACTERIOCHLOROPHYLL A / PHOTOSYNTHESIS
Function / homology
Function and homology information


organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / metal ion binding / plasma membrane
Similarity search - Function
Light-harvesting complex / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #250 / Light-harvesting Protein / Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit / Antenna complex, beta domain superfamily / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Light-harvesting protein B beta chain ...Light-harvesting complex / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #250 / Light-harvesting Protein / Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit / Antenna complex, beta domain superfamily / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Light-harvesting protein B beta chain / Antenna complex, alpha/beta subunit / Light-harvesting complex / Antenna complex alpha/beta subunit / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Few Secondary Structures / Irregular / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL A / BENZAMIDINE / Rhodopin b-D-glucoside / Light-harvesting protein B-800/850 alpha chain / Light-harvesting protein B-800/850 beta chain
Similarity search - Component
Biological speciesRhodoblastus acidophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsPapiz, M.Z. / Prince, S.M. / Howard, T. / Cogdell, R.J. / Isaacs, N.W.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: The structure and thermal motion of the B800-850 LH2 complex from Rps. acidophila at 2.0 A resolution and 100K : new structural features and functionally relevant motions.
Authors: Papiz, M.Z. / Prince, S.M. / Howard, T. / Cogdell, R.J. / Isaacs, N.W.
#1: Journal: Nature / Year: 1995
Title: Crystal structure of an integral membrane light-harvesting complex from photosynthetic bacteria.
Authors: McDermott, G. / Prince, S.M. / Freer, A.A. / Hawthornthwaite-Lawless, A.M. / Papiz, M.Z. / Cogdell, R.J. / Isaacs, N.W.
#2: Journal: Structure / Year: 1996
Title: Pigment-pigment interactions and energy transfer in the antenna complex of the photosynthetic bacterium Rps. acidophila.
Authors: Freer, A.A. / Prince, S.M. / Sauer, K. / Papiz, M.Z. / Hawthornthwaite-Lawless, A.M. / McDermott, G. / Cogdell, R.J. / Isaacs, N.W.
#3: Journal: J.Mol.Biol. / Year: 1997
Title: Apoprotein Structure in the LH2 complex from Rhodopseudomonas acidophila Strain 10050: Modular assembly and protein pigment interactions
Authors: Prince, S.M. / Papiz, M.Z. / Freer, A.A. / McDermott, G. / Hawthornthwaite-Lawless, A.M. / Cogdell, R.J. / Isaacs, N.W.
History
DepositionJan 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Apr 16, 2014Group: Data collection
Revision 1.4Mar 30, 2016Group: Non-polymer description
Revision 1.5Feb 1, 2017Group: Structure summary
Revision 1.6Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.7Aug 16, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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.beg_label_asym_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_seq_id
Revision 1.8Mar 13, 2024Group: Data collection / Source and taxonomy / Category: chem_comp_atom / chem_comp_bond / entity_src_gen
Item: _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_bond.pdbx_aromatic_flag
Remark 11SEQUENCE FOR REFINEMENT OF NCS AND TLS GROUPS IT WAS NECESSARY TO GIVE ALL ATOMS CHAIN IDENTIFIERS. ...SEQUENCE FOR REFINEMENT OF NCS AND TLS GROUPS IT WAS NECESSARY TO GIVE ALL ATOMS CHAIN IDENTIFIERS. TO CONFORM TO PDB NAMIING CONVENTIONS MOLECULES WHICH HAVE BEEN REDEFINED AS HETATM's IN THIS DEPOSITION HAVE HAD THEIR CHAIN ID'S REMOVED AND RESIDUES RENUMBERED. IT IS POSSIBLE TO RELATE THE NCS AND TLS IDENTIFIERS ABOVE WITH THE NEW HETATM RESIDUE NUMBERS IN THE FOLLOWING WAY: ATOM CHAIN RESIDUE HETATM RESIDUE 1 1 301 2 1 302 3 1 303 4 1 304 5 1 305 6 1 306 7 1 307 8 1 308 9 1 309 S 1 401 T 1 402 U 1 403 V 1 404 X 1 405 Y 1 406

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Light-harvesting protein B-800/850, alpha chain
B: Light-harvesting protein B-800/850, beta chain
C: Light-harvesting protein B-800/850, alpha chain
D: Light-harvesting protein B-800/850, beta chain
E: Light-harvesting protein B-800/850, alpha chain
F: Light-harvesting protein B-800/850, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,39430
Polymers30,7866
Non-polymers14,60824
Water4,143230
1
A: Light-harvesting protein B-800/850, alpha chain
B: Light-harvesting protein B-800/850, beta chain
C: Light-harvesting protein B-800/850, alpha chain
D: Light-harvesting protein B-800/850, beta chain
E: Light-harvesting protein B-800/850, alpha chain
F: Light-harvesting protein B-800/850, beta chain
hetero molecules

A: Light-harvesting protein B-800/850, alpha chain
B: Light-harvesting protein B-800/850, beta chain
C: Light-harvesting protein B-800/850, alpha chain
D: Light-harvesting protein B-800/850, beta chain
E: Light-harvesting protein B-800/850, alpha chain
F: Light-harvesting protein B-800/850, beta chain
hetero molecules

A: Light-harvesting protein B-800/850, alpha chain
B: Light-harvesting protein B-800/850, beta chain
C: Light-harvesting protein B-800/850, alpha chain
D: Light-harvesting protein B-800/850, beta chain
E: Light-harvesting protein B-800/850, alpha chain
F: Light-harvesting protein B-800/850, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,18290
Polymers92,35718
Non-polymers43,82572
Water32418
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area103020 Å2
ΔGint-512 kcal/mol
Surface area36200 Å2
MethodPISA
2
A: Light-harvesting protein B-800/850, alpha chain
B: Light-harvesting protein B-800/850, beta chain
C: Light-harvesting protein B-800/850, alpha chain
D: Light-harvesting protein B-800/850, beta chain
E: Light-harvesting protein B-800/850, alpha chain
F: Light-harvesting protein B-800/850, beta chain
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)272,365180
Polymers184,71536
Non-polymers87,650144
Water64936
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area215350 Å2
ΔGint-1073 kcal/mol
Surface area63090 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)117.052, 117.052, 298.438
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
12B
22D
32F
13A
23C
33E
14B
24D
34F
15A
25C
35E
16B
26D
36F
17A
27C
37E

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
11CXMCXMALAALA4AA1 - 531 - 53
21CXMCXMALAALA4CC1 - 531 - 53
31CXMCXMALAALA4EE1 - 531 - 53
12ALAALAHISHIS4BB1 - 411 - 41
22ALAALAHISHIS4DD1 - 411 - 41
32ALAALAHISHIS4FF1 - 411 - 41
13BCLBCLBCLBCL1AI301
23BCLBCLBCLBCL1CQ303
33BCLBCLBCLBCL1EZ305
14BCLBCLBCLBCL1BL302
24BCLBCLBCLBCL1DU304
34BCLBCLBCLBCL1FDA306
15BCLBCLBCLBCL1AJ307
25BCLBCLBCLBCL1CR308
35BCLBCLBCLBCL1EAA309
16RG1RG1RG1RG11BK401
26RG1RG1RG1RG11DT402
36RG1RG1RG1RG11CM403
17RG1RG1RG1RG11AG404
27RG1RG1RG1RG11CN405
37RG1RG1RG1RG11EV406

NCS ensembles :
ID
1
2
3
4
5
6
7
DetailsThe biological assembly is a nonamer generated, from three copies in the asymmetric unit, by the operations: -y, x-y, z and y-x, -x, z.

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Components

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Light-harvesting protein B-800/850, ... , 2 types, 6 molecules ACEBDF

#1: Protein Light-harvesting protein B-800/850, alpha chain / Antenna pigment protein / alpha chain


Mass: 5702.733 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: cell membrane / Source: (natural) Rhodoblastus acidophilus (bacteria) / Strain: 10050 / References: UniProt: P26789
#2: Protein/peptide Light-harvesting protein B-800/850, beta chain / Antenna pigment protein / beta chain


Mass: 4559.203 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rhodoblastus acidophilus (bacteria) / Strain: 10050 / References: UniProt: P26790

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Sugars , 2 types, 12 molecules

#3: Sugar
ChemComp-RG1 / Rhodopin b-D-glucoside / (3E)-3,4-didehydro-1',2'-dihydro-psi,psi-caroten-1'-yl beta-D-glucopyranoside


Type: D-saccharide / Mass: 715.013 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C46H66O6
#4: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Antenna pigment protein / beta chain / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 3 types, 242 molecules

#5: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A / Bacteriochlorophyll


Mass: 911.504 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C55H74MgN4O6
#6: Chemical ChemComp-BEN / BENZAMIDINE / Benzamidine


Mass: 120.152 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H8N2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 4.05 Å3/Da / Density % sol: 69.36 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9.3
Details: 1.0 M Phosphate, 2.5% Benzamidine, 0.75 % Beta-octylglucoside, 25-250 mM NaCl equilibrated against 2.3 M Ammonium Sulphate at pH 9.5, pH 9.3, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 9.5 / Method: vapor diffusion / Details: Papiz, M.Z., (1989) J. Mol. Biol., 209, 833.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.9 Mphosphate1drop
23 %benzamidine hydrochloride1drop
32.4 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 25, 1997
Details: VERTICALLY FOCUSING 1.2M Si MIRROR, MONOCHROMATED WITH A HORIZONTALLY FOCUSED Si(111) CRYSTAL
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2→33 Å / Num. all: 49320 / Num. obs: 48976 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 8.7
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 2.5 / % possible all: 95
Reflection
*PLUS
% possible obs: 99.3 % / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
Num. unique obs: 2431

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
DMmodel building
REFMAC5.1.24refinement
CCP4(SCALA)data scaling
DMphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1KZU

1kzu


Resolution: 2→8 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.027 / SU ML: 0.058 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: Combined TLS and Isotropic refinement
Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19006 2431 4.7 %RANDOM
Rwork0.16943 ---
obs0.1704 48976 99.3 %-
all-52374 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.962 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å20.51 Å20 Å2
2--1.03 Å20 Å2
3----1.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.105 Å0.109 Å
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2178 0 1053 230 3461
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0213335
X-RAY DIFFRACTIONr_bond_other_d0.0140.023170
X-RAY DIFFRACTIONr_angle_refined_deg1.6212.2864642
X-RAY DIFFRACTIONr_angle_other_deg1.50837235
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4845273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.5120.2531
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.023356
X-RAY DIFFRACTIONr_gen_planes_other0.040.02632
X-RAY DIFFRACTIONr_nbd_refined0.2740.2778
X-RAY DIFFRACTIONr_nbd_other0.2690.23729
X-RAY DIFFRACTIONr_nbtor_other0.1070.21398
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3420.2185
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3580.262
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3690.2224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4080.244
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.8451.51407
X-RAY DIFFRACTIONr_mcangle_it1.48722250
X-RAY DIFFRACTIONr_scbond_it1.94131928
X-RAY DIFFRACTIONr_scangle_it2.614.52386
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
31A141tight positional0.020.05
32C141tight positional0.020.05
33E141tight positional0.020.05
41B141tight positional0.020.05
42D141tight positional0.020.05
43F141tight positional0.020.05
51A141tight positional0.020.05
52C141tight positional0.020.05
53E141tight positional0.020.05
61B116tight positional0.020.05
62D116tight positional0.020.05
63F116tight positional0.020.05
71A88tight positional0.260.05
72C88tight positional0.130.05
73E88tight positional0.130.05
11A799medium positional0.150.5
12C799medium positional0.250.5
13E799medium positional0.160.5
21B626medium positional0.10.5
22D626medium positional0.080.5
23F626medium positional0.080.5
31A141tight thermal0.110.5
32C141tight thermal0.120.5
33E141tight thermal0.120.5
41B141tight thermal0.130.5
42D141tight thermal0.10.5
43F141tight thermal0.120.5
51A141tight thermal0.10.5
52C141tight thermal0.10.5
53E141tight thermal0.090.5
61B116tight thermal0.090.5
62D116tight thermal0.110.5
63F116tight thermal0.130.5
71A88tight thermal0.080.5
72C88tight thermal0.050.5
73E88tight thermal0.050.5
11A799medium thermal0.352
12C799medium thermal0.352
13E799medium thermal0.322
21B626medium thermal0.432
22D626medium thermal0.412
23F626medium thermal0.332
LS refinement shellResolution: 2→2.049 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.208 170
Rwork0.184 3408
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)
15.78611.5384-1.56323.6982-0.10272.741-0.0087-0.44730.15160.427-0.1124-0.248-0.13430.35850.1210.1828-0.0817-0.13240.2819-0.01090.168523.2779.89943.949
21.08430.3016-0.39621.02950.796412.87790.0913-0.09910.02380.0936-0.0275-0.08710.0656-0.0528-0.06370.0718-0.0247-0.0420.14480.02820.090217.8890.18325.707
33.08521.395-0.20612.4243-1.58355.4563-0.25730.4113-0.3159-1.17420.1516-0.73550.43270.51330.10560.2004-0.00110.07270.2633-0.01340.150624.255-9.183.274
442.543821.68884.945713.0004-2.867415.6993-0.0506-0.98610.22570.30490.00720.3566-0.1962-0.20240.04340.3174-0.0687-0.11490.30550.00210.169822.8746.38152.077
50.8330.24290.27341.29771.337111.71120.05210.0043-0.02420.1311-0.049-0.31730.06630.8325-0.0030.0721-0.0382-0.09020.32610.04710.200131.6361.81331.737
611.1729-6.7754-3.461710.8808-0.102811.94750.32880.12270.3634-0.5962-0.1598-0.4978-0.36580.7121-0.16890.1165-0.04510.0630.41720.01560.2631.5912.1458.12
71.68761.1380.0473.73070.98382.46980.0019-0.17080.03510.0881-0.0016-0.22510.19090.2951-0.00020.08920.0165-0.04840.20040.04640.110423.755-5.08423.557
83.39561.1086-1.19387.0881-1.850312.13940.09-0.23110.18980.428-0.107-0.1925-0.65540.52020.0170.1032-0.0584-0.05010.23110.01060.133626.9176.04622.465
914.7662.0545-3.0632.19563.83677.414-0.05350.8303-0.3323-0.29590.167-0.3806-0.49670.0864-0.11350.2013-0.0821-0.07680.30950.03360.195228.29810.65530.765
102.021-0.74472.59865.8864-2.5262.80010.0889-0.0987-0.05720.3515-0.0407-0.3832-0.14110.2147-0.04830.0884-0.0348-0.07120.26640.01690.125624.1752.6132.399
112.54441.07740.1175.348-1.80764.5078-0.1202-0.44530.25880.24640.0584-0.0552-0.43020.01190.06170.2283-0.0465-0.07590.279-0.10380.1511.49422.75243.914
121.13150.1352-0.34180.92280.665415.05570.0247-0.11150.10050.0748-0.0618-0.0130.0532-0.02990.0370.0869-0.0454-0.04350.1182-0.00930.086113.5611.67525.718
135.0124-2.43511.459110.2894-1.31425.03830.15530.52210.1646-1.0856-0.2571-0.7795-0.06670.7120.10180.2141-0.03640.07320.25480.04010.1324.478.5333.272
144.254613.02772.931342.8754-2.257112.33180.2612-0.8173-0.0420.3365-0.25850.6903-0.14630.0616-0.00270.3052-0.0212-0.07230.4639-0.07550.177313.38119.87652.07
151.48680.1361-0.56081.16080.63289.3143-0.0493-0.12850.15440.0838-0.0009-0.2242-0.4790.56220.05030.1755-0.1308-0.09420.2133-0.02260.16823.0621.76631.739
1619.0544-3.2887-3.28937.10651.223915.17320.42340.55210.2291-0.374-0.2384-0.0366-0.9590.1754-0.18490.2985-0.15520.04410.25590.05790.249522.84221.8918.115
171.5641-0.47270.51222.70690.95643.55090.0351-0.10850.11770.0617-0.0415-0.1555-0.02150.36850.00650.0914-0.0611-0.05530.1749-0.00270.105421.42211.35923.558
183.2907-0.74170.82696.5185-1.942813.4694-0.0341-0.22340.3480.33290.0407-0.0377-0.9072-0.0511-0.00660.1746-0.0738-0.05070.1715-0.03140.145516.75221.94722.447
199.74017.22-5.522510.18122.18449.6004-0.29490.3736-0.1293-0.83420.4378-0.5457-0.7079-0.1846-0.14290.3092-0.0828-0.06440.2011-0.05070.195614.85426.41630.731
201.0354-1.3312-0.88122.36520.0884-0.9485-0.1658-0.2210.2620.0989-0.0149-0.2659-0.3609-0.02570.18070.135-0.0848-0.05080.1956-0.02850.131416.79617.55232.388
213.4097-0.5226-0.61064.8744-0.97233.3374-0.047-0.65760.34980.3073-0.01020.1439-0.4569-0.08630.05710.23930.0426-0.01140.2787-0.15150.1648-5.7524.84443.929
221.15890.1659-0.62680.986-0.075712.5230.0196-0.140.09160.07510.0230.0538-0.00710.0182-0.04260.1148-0.0031-0.02850.1004-0.03920.08892.89917.71125.719
238.6244-1.8711.52455.67860.63365.88970.14180.91590.5426-0.6346-0.2848-0.4148-0.53990.52280.14310.2617-0.03330.01410.21630.07660.125713.23522.2793.293
249.013-16.26862.870647.1547-1.55438.64180.6425-0.4893-0.26010.9928-0.9990.5151-0.2753-0.03730.35650.3337-0.0433-0.02410.5119-0.11870.1423-2.5123.93252.115
251.87660.4516-1.77061.2498-0.19999.2564-0.006-0.24390.31680.0758-0.0593-0.0702-0.86330.23390.06530.3278-0.0137-0.0590.1097-0.1020.20893.67131.56931.745
2615.59655.7647-1.84478.0616-0.477911.2701-0.00030.4720.5512-0.31690.25780.3891-0.5948-0.2259-0.25750.4082-0.01670.0040.12850.06840.27673.4231.458.123
273.5315-0.7906-1.03461.46531.22853.29220.0267-0.16690.22080.0326-0.0448-0.0509-0.19260.18210.01810.1721-0.0526-0.05930.1081-0.03960.09789.11322.51723.544
285.4276-1.10422.46744.3573-0.345913.482-0.0972-0.45390.27750.20840.02560.1248-0.5681-0.73610.07160.21770.0108-0.03030.1427-0.05890.1437-1.30727.61122.448
291.7513-0.9384-3.917815.71210.40065.11580.11910.27690.3819-1.0270.0457-0.3659-0.4382-0.4705-0.16480.33860.032-0.02040.2451-0.07780.2149-5.57529.80630.731
307.96781.84828.75393.40024.976514.7125-0.1355-0.46720.51060.0024-0.0851-0.0176-0.5105-0.37580.22060.1965-0.0326-0.00780.1403-0.06240.12531.60224.34232.386
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 121 - 12
2X-RAY DIFFRACTION2AA13 - 3713 - 37
3X-RAY DIFFRACTION3AA38 - 5338 - 53
4X-RAY DIFFRACTION4BB1 - 61 - 6
5X-RAY DIFFRACTION5BB7 - 347 - 34
6X-RAY DIFFRACTION6BB35 - 4135 - 41
7X-RAY DIFFRACTION7AS3011
8X-RAY DIFFRACTION8BT3021
9X-RAY DIFFRACTION9AY3071
10X-RAY DIFFRACTION10BG4011
11X-RAY DIFFRACTION11CC1 - 121 - 12
12X-RAY DIFFRACTION12CC13 - 3713 - 37
13X-RAY DIFFRACTION13CC38 - 5338 - 53
14X-RAY DIFFRACTION14DD1 - 61 - 6
15X-RAY DIFFRACTION15DD7 - 347 - 34
16X-RAY DIFFRACTION16DD35 - 4135 - 41
17X-RAY DIFFRACTION17CU3031
18X-RAY DIFFRACTION18DV3041
19X-RAY DIFFRACTION19CZ3081
20X-RAY DIFFRACTION20DH4021
21X-RAY DIFFRACTION21EE1 - 121 - 12
22X-RAY DIFFRACTION22EE13 - 3713 - 37
23X-RAY DIFFRACTION23EE38 - 5338 - 53
24X-RAY DIFFRACTION24FF1 - 61 - 6
25X-RAY DIFFRACTION25FF7 - 347 - 34
26X-RAY DIFFRACTION26FF35 - 4135 - 41
27X-RAY DIFFRACTION27EW3051
28X-RAY DIFFRACTION28FX3061
29X-RAY DIFFRACTION29EAA3091
30X-RAY DIFFRACTION30CI4031
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.194 / Rfactor Rwork: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.019
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.62

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