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- PDB-4pog: MCM-ssDNA co-crystal structure -

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Basic information

Entry
Database: PDB / ID: 4pog
TitleMCM-ssDNA co-crystal structure
Components
  • 30-mer oligo(dT)
  • Cell division control protein 21
KeywordsREPLICATION / DNA BINDING PROTEIN/DNA / OB-fold / DNA replication / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


single-stranded 3'-5' DNA helicase activity / MCM complex / intein-mediated protein splicing / double-strand break repair via break-induced replication / DNA unwinding involved in DNA replication / single-stranded DNA binding / endonuclease activity / DNA helicase / cell division / ATP binding / metal ion binding
Similarity search - Function
mini-chromosome maintenance (MCM) complex, chain A, domain 1 / mini-chromosome maintenance (MCM) complex, chain A, domain 1 / Rubrerythrin, domain 2 - #10 / Intein splicing domain / Intein / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal ...mini-chromosome maintenance (MCM) complex, chain A, domain 1 / mini-chromosome maintenance (MCM) complex, chain A, domain 1 / Rubrerythrin, domain 2 - #10 / Intein splicing domain / Intein / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / MCM N-terminal domain / MCM N-terminal domain / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / MCM OB domain / MCM OB domain / Mini-chromosome maintenance protein / MCM, AAA-lid domain / MCM P-loop domain / MCM AAA-lid domain / MCM family domain profile. / minichromosome maintenance proteins / MCM domain / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily / Rubrerythrin, domain 2 / Single Sheet / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA helicase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.203 Å
AuthorsFroelich, C.A. / Kang, S. / Epling, L.B. / Bell, S.P. / Enemark, E.J.
CitationJournal: Elife / Year: 2014
Title: A conserved MCM single-stranded DNA binding element is essential for replication initiation.
Authors: Froelich, C.A. / Kang, S. / Epling, L.B. / Bell, S.P. / Enemark, E.J.
History
DepositionFeb 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_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_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division control protein 21
B: Cell division control protein 21
C: Cell division control protein 21
D: Cell division control protein 21
E: Cell division control protein 21
F: Cell division control protein 21
G: Cell division control protein 21
H: Cell division control protein 21
I: Cell division control protein 21
J: Cell division control protein 21
K: Cell division control protein 21
L: Cell division control protein 21
X: 30-mer oligo(dT)
V: 30-mer oligo(dT)
Y: 30-mer oligo(dT)
Z: 30-mer oligo(dT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)389,91728
Polymers389,13216
Non-polymers78512
Water00
1
A: Cell division control protein 21
B: Cell division control protein 21
C: Cell division control protein 21
D: Cell division control protein 21
E: Cell division control protein 21
F: Cell division control protein 21
X: 30-mer oligo(dT)
Z: 30-mer oligo(dT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,95814
Polymers194,5668
Non-polymers3926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14380 Å2
ΔGint-72 kcal/mol
Surface area73850 Å2
MethodPISA
2
G: Cell division control protein 21
H: Cell division control protein 21
I: Cell division control protein 21
J: Cell division control protein 21
K: Cell division control protein 21
L: Cell division control protein 21
V: 30-mer oligo(dT)
Y: 30-mer oligo(dT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,95814
Polymers194,5668
Non-polymers3926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14820 Å2
ΔGint-69 kcal/mol
Surface area75130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.277, 113.398, 196.855
Angle α, β, γ (deg.)90.00, 101.35, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 4 / Auth seq-ID: 0 - 254 / Label seq-ID: 1 - 255

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH
9II
10JJ
11KK
12LL

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Components

#1: Protein
Cell division control protein 21 / MCM


Mass: 29400.711 Da / Num. of mol.: 12 / Fragment: N-terminal domain (UNP residues 2-256)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: Cdc21, PF0482 / Plasmid: pRSFduet pLE009.3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL / References: UniProt: Q8U3I4
#2: DNA chain
30-mer oligo(dT)


Mass: 9080.827 Da / Num. of mol.: 4 / Source method: obtained synthetically
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn

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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: 2.65 Å3/Da / Density % sol: 53.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50 mM MES, pH 6.0, 10 mM magnesium acetate, 28.5% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 30, 2010
RadiationMonochromator: Rosenbaum-Rock double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.203→50 Å / Num. all: 66924 / Num. obs: 66920 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 13.4
Reflection shellResolution: 3.203→3.31 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.786 / Mean I/σ(I) obs: 1.64 / Num. unique all: 6626 / % possible all: 100

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4POF
Resolution: 3.203→48.51 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.869 / SU B: 80.109 / SU ML: 0.585 / Cross valid method: THROUGHOUT / ESU R Free: 0.601 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29399 3376 5 %RANDOM
Rwork0.25691 ---
obs0.25877 63497 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 129.847 Å2
Baniso -1Baniso -2Baniso -3
1-9.84 Å20 Å21.93 Å2
2---5.38 Å20 Å2
3----3.7 Å2
Refinement stepCycle: LAST / Resolution: 3.203→48.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24346 584 12 0 24942
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02225455
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1642.00334490
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.55453039
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.79424.641207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.277154610
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.11915188
X-RAY DIFFRACTIONr_chiral_restr0.0710.23927
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02118902
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it12.0351.515242
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it16.941224884
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.284310213
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.2674.59606
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1731 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.670.5
Bmedium positional0.420.5
Cmedium positional0.390.5
Dmedium positional0.760.5
Emedium positional0.510.5
Fmedium positional0.540.5
Gmedium positional1.240.5
Hmedium positional0.460.5
Imedium positional0.580.5
Jmedium positional0.840.5
Kmedium positional0.80.5
Lmedium positional0.490.5
Amedium thermal9.542
Bmedium thermal7.352
Cmedium thermal6.432
Dmedium thermal8.042
Emedium thermal14.052
Fmedium thermal6.552
Gmedium thermal20.942
Hmedium thermal27.022
Imedium thermal24.772
Jmedium thermal12.022
Kmedium thermal9.42
Lmedium thermal11.732
LS refinement shellResolution: 3.203→3.286 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 218 -
Rwork0.372 4453 -
obs-4671 95.29 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
16.44572.3132.15438.68884.29767.6234-0.37470.96361.2853-0.57470.6649-0.4976-1.01710.9883-0.29021.2269-0.42980.21110.78040.15660.8356-7.3877104.6709168.3457
23.474-1.7336-0.49923.17121.75422.0330.19170.1611-0.0002-0.62890.02660.1332-0.0987-0.074-0.21830.804-0.0907-0.01840.9930.02110.7551-20.745684.154167.3329
311.595-2.86954.7923.0327-2.72854.4649-0.30150.31930.11870.4160.2842-0.3716-0.20720.57450.01740.7871-0.1068-0.02180.9087-0.22930.7805-1.03981.0508187.4509
46.7218-1.9897-0.3497.05790.51384.87440.55320.40490.182-1.5-0.443-0.6201-0.26410.1665-0.11021.29190.06350.17870.72120.11210.4597-8.175666.1267135.502
53.3261-2.61820.2557.0138-1.89583.16950.0438-0.2975-0.23270.12310.04540.70510.114-0.3989-0.08930.8889-0.0686-0.06280.85750.02460.8116-20.402356.0491154.4621
611.18683.48694.8932.28451.50434.427-0.10020.1377-0.6432-0.29220.5719-0.3653-0.98750.234-0.47170.6688-0.06280.07240.8572-0.23160.83171.240271.9993163.729
72.9230.5759-0.47335.3132-0.17428.8665-0.4403-0.20790.0643-0.2049-0.0635-0.22941.20740.40780.50371.2120.30440.4020.63670.09260.6753-6.196819.5142152.7183
81.04380.09070.20780.1261-0.96729.3857-0.4873-0.13590.1315-0.07370.0293-0.12580.3692-0.73660.4581.1270.10580.15970.88460.00790.755-20.286529.9389170.0136
910.87920.77070.42794.82161.56640.5795-0.2161-0.320.1149-0.07060.0181-0.3162-0.04930.10550.1980.8718-0.0158-0.2190.98090.39990.9111.721246.8138163.325
104.9518-0.36671.3887.60230.34944.21730.3997-0.614-0.5082-0.5803-0.16-0.50320.63260.4826-0.23960.92920.18860.04760.68340.25040.8236-10.29859.1014201.8357
112.3769-0.41610.14334.88660.5820.91720.2023-0.0298-0.032-0.2856-0.20970.0771-0.10540.01760.00730.86560.064-0.00320.84350.0080.7499-23.86829.333199.8246
1214.72664.4106-2.92532.96690.27756.3905-0.1985-0.48290.4174-0.4682-0.1750.12610.30161.29250.37350.77520.2110.0971.05490.35830.62190.087733.4243184.9573
135.5521.91311.851710.1208-0.80312.52440.5949-0.50.14051.8363-0.4018-0.63820.1580.0258-0.19311.9924-0.3213-0.05640.56980.01920.1686-18.870247.2385234.0484
142.39333.76660.40949.2094-2.42543.01660.13780.08110.20730.58540.04830.7771-0.2439-0.0378-0.1861.31830.01910.22710.7167-0.03370.8142-26.78757.2272212.6539
158.2597-3.1004-1.93076.239-2.16242.26250.19270.53510.32920.6049-0.6839-1.7441-0.45860.1370.49120.8291-0.2137-0.14630.84280.14331.2341-3.166942.285208.5454
164.99161.0344-0.23722.16340.63828.386-0.01310.04020.17680.8291-0.2786-0.3731-0.12450.13270.29171.5577-0.0107-0.09520.5239-0.12490.4818-16.165694.0528217.6692
172.09190.2122-1.32760.30770.61464.4403-0.02590.1154-0.17250.30750.026-0.1740.1802-0.65801.0368-0.08360.06390.9319-0.05320.7011-24.403783.0561197.1083
1812.0629-5.59810.54954.1544-1.85652.8053-0.3192-0.2907-0.39810.784-0.4417-0.44720.36310.46190.76091.4103-0.0443-0.10190.70670.10540.7686-3.482967.7895209.3067
196.73041.7453-2.44442.92542.81329.638-0.48460.1197-0.21020.435-0.09170.8430.0606-0.53070.57631.55160.07970.66180.290.14280.8146-6.72799.3092135.6106
201.7743-2.8752-0.796710.84832.0240.5611-0.85480.4927-0.03112.36920.83370.88630.45630.19720.02111.44870.21210.43911.06860.19180.79129.41599.044117.643
2116.1031-2.24465.63047.1951-2.00912.31030.21820.5537-0.03480.9044-0.27531.53410.04510.43950.05720.75430.12680.68970.52930.13691.4359-11.6792117.5067112.867
224.63032.80111.23416.59450.32286.6177-0.03230.2057-0.16341.1476-0.52611.7551.6320.19630.55840.9510.03360.71380.38660.10791.4183-1.09764.5141101.9022
232.84190.4342-0.59244.02160.74652.9196-0.0032-0.09570.16940.4550.15420.78950.1590.6909-0.1510.23730.0676-0.04650.93110.17521.006212.700482.524692.4133
2410.2441-6.02462.07799.95857.117511.4177-1.33081.4537-2.2650.6659-1.77613.9075-0.1841-0.60993.10690.1904-0.09530.42770.4166-0.55592.7828-11.259593.669103.3093
253.72380.88712.136416.27611.115810.3725-0.14890.1604-0.0595-3.21180.22091.06351.82410.0024-0.0722.8229-0.3608-0.76740.08680.13050.2717.133577.406853.5257
261.0588-0.47630.61524.953-4.75174.8194-0.0192-0.41940.1559-1.3373-0.6475-0.30840.88790.78810.66681.2909-0.0037-0.17840.83890.18780.824617.612196.106765.741
279.0976-1.23270.96112.2645-4.819911.99970.6006-0.1462-0.2265-0.22751.16331.1806-0.1996-1.5333-1.76390.5505-0.2833-0.69451.06030.85141.7004-7.118290.422278.0955
283.7399-1.7128-0.215712.07283.32966.61920.2355-0.25180.1608-1.63970.097-0.2012-0.0754-0.2724-0.33251.3989-0.2321-0.11950.42980.04270.56212.7749125.968240.7091
293.0264-3.9906-0.93849.21892.02573.0937-0.2106-0.3617-0.03550.6330.3068-0.74510.1853-0.0107-0.09621.1179-0.1953-0.34480.618-0.01620.969719.7685126.114964.4879
3018.5825.3946-2.30112.6695-2.19982.6412-0.1931-0.53740.0158-0.20030.2655-0.10980.4567-0.3516-0.07231.2189-0.1167-0.59010.53370.15250.7536-3.6162109.853863.0103
314.4612-0.7936-2.10074.6559-0.94728.10470.07210.06030.2254-0.95860.24760.4256-0.8976-0.3711-0.31981.2686-0.1146-0.150.48120.09960.72747.8541161.643675.9973
320.66460.1441-1.21563.9815-2.71063.968-0.079-0.1737-0.0269-0.46770.14240.14440.15340.3063-0.06340.3936-0.1604-0.18430.94730.0060.849615.696142.678689.73
3311.09681.75523.30442.25493.41945.35790.3257-0.0935-0.1699-0.4067-0.29620.0986-0.2221-0.5389-0.02951.0719-0.1959-0.50730.64840.26250.8231-3.9989135.166670.5593
344.6418-1.11710.21744.503-0.42917.0095-0.06670.12860.14050.66240.0080.4483-0.53780.03270.05880.42620.05070.1190.79560.08710.8928-3.7465149.1604123.3738
350.88521.5866-0.39394.02770.7833.0527-0.21580.04750.10020.42570.15710.31760.90440.75850.05870.69050.20180.1561.04270.15730.838510.2879130.1676116.6939
368.54492.37775.48174.3012-2.538210.6633-0.64210.11210.1192-0.39980.90350.93870.4448-0.9841-0.26140.3893-0.1475-0.07140.9630.15151.1223-8.1529136.466695.8327
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 100
2X-RAY DIFFRACTION2A101 - 127
3X-RAY DIFFRACTION2A183 - 254
4X-RAY DIFFRACTION3A128 - 182
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