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- PDB-1yrq: Structure of the ready oxidized form of [NiFe]-hydrogenase -

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Basic information

Entry
Database: PDB / ID: 1yrq
TitleStructure of the ready oxidized form of [NiFe]-hydrogenase
Components(Periplasmic [NiFe] hydrogenase ...) x 2
KeywordsOXIDOREDUCTASE / NiB state / hydroxide bridge
Function / homology
Function and homology information


cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space ...cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / membrane / metal ion binding
Similarity search - Function
Cytochrome-c3 Hydrogenase; Chain A, domain 2 / Cytochrome-c3 hydrogenase, C-terminal domain / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / : / [NiFe]-hydrogenase, small subunit / Cytochrome-c3 hydrogenase, C-terminal / [NiFe]-hydrogenase, small subunit, C-terminal domain superfamily / NiFe/NiFeSe hydrogenase small subunit C-terminal ...Cytochrome-c3 Hydrogenase; Chain A, domain 2 / Cytochrome-c3 hydrogenase, C-terminal domain / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / : / [NiFe]-hydrogenase, small subunit / Cytochrome-c3 hydrogenase, C-terminal / [NiFe]-hydrogenase, small subunit, C-terminal domain superfamily / NiFe/NiFeSe hydrogenase small subunit C-terminal / Nickel-dependent hydrogenases large subunit signature 2. / Nickel-dependent hydrogenases large subunit signature 1. / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Nickel-dependent hydrogenase, large subunit, nickel binding site / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Few Secondary Structures / Irregular / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FE3-S4 CLUSTER / CARBONMONOXIDE-(DICYANO) IRON / NICKEL (II) ION / IRON/SULFUR CLUSTER / Periplasmic [NiFe] hydrogenase small subunit / Periplasmic [NiFe] hydrogenase large subunit
Similarity search - Component
Biological speciesDesulfovibrio fructosovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsVolbeda, A. / Martin, L. / Cavazza, C. / Matho, M. / Faber, B.W. / Roseboom, W. / Albracht, S.P. / Garcin, E. / Rousset, M. / Fontecilla-Camps, J.C.
Citation
Journal: J.Biol.Inorg.Chem. / Year: 2005
Title: Structural differences between the ready and unready oxidized states of [NiFe] hydrogenases.
Authors: Volbeda, A. / Martin, L. / Cavazza, C. / Matho, M. / Faber, B.W. / Roseboom, W. / Albracht, S.P. / Garcin, E. / Rousset, M. / Fontecilla-Camps, J.C.
#1: Journal: Int.J.Hydrogen Energy / Year: 2002
Title: High-resolution crystallographic analysis of Desulfovibrio fructosovorans [NiFe] hydrogenase
Authors: Volbeda, A. / Montet, Y. / Vernede, X. / Hatchikian, E.C. / Fontecilla-Camps, J.C.
#2: Journal: Nat.Struct.Biol. / Year: 1997
Title: Gas access to the active site of Ni-Fe hydrogenase probed by X-ray crystallography and molecular dynamics
Authors: Montet, Y. / Amara, P. / Volbeda, A. / Vernede, X. / Hatchikian, E.C. / Field, M.J. / Frey, M. / Fontecilla-Camps, J.C.
History
DepositionFeb 4, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name
Revision 1.4Aug 23, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_conn_type.id / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 6, 2023Group: Data collection / Derived calculations / Category: struct_biol / struct_conn / struct_conn_type
Revision 1.6Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Periplasmic [NiFe] hydrogenase small subunit
H: Periplasmic [NiFe] hydrogenase large subunit
B: Periplasmic [NiFe] hydrogenase small subunit
I: Periplasmic [NiFe] hydrogenase large subunit
C: Periplasmic [NiFe] hydrogenase small subunit
J: Periplasmic [NiFe] hydrogenase large subunit
D: Periplasmic [NiFe] hydrogenase small subunit
K: Periplasmic [NiFe] hydrogenase large subunit
F: Periplasmic [NiFe] hydrogenase small subunit
M: Periplasmic [NiFe] hydrogenase large subunit
G: Periplasmic [NiFe] hydrogenase small subunit
N: Periplasmic [NiFe] hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)535,51548
Polymers528,20812
Non-polymers7,30836
Water33,9761886
1
A: Periplasmic [NiFe] hydrogenase small subunit
H: Periplasmic [NiFe] hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,2538
Polymers88,0352
Non-polymers1,2186
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8580 Å2
ΔGint-122 kcal/mol
Surface area25420 Å2
MethodPISA, PQS
2
B: Periplasmic [NiFe] hydrogenase small subunit
I: Periplasmic [NiFe] hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,2538
Polymers88,0352
Non-polymers1,2186
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8590 Å2
ΔGint-119 kcal/mol
Surface area25370 Å2
MethodPISA, PQS
3
C: Periplasmic [NiFe] hydrogenase small subunit
J: Periplasmic [NiFe] hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,2538
Polymers88,0352
Non-polymers1,2186
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8510 Å2
ΔGint-122 kcal/mol
Surface area25230 Å2
MethodPISA, PQS
4
D: Periplasmic [NiFe] hydrogenase small subunit
K: Periplasmic [NiFe] hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,2538
Polymers88,0352
Non-polymers1,2186
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8580 Å2
ΔGint-120 kcal/mol
Surface area25210 Å2
MethodPISA, PQS
5
F: Periplasmic [NiFe] hydrogenase small subunit
M: Periplasmic [NiFe] hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,2538
Polymers88,0352
Non-polymers1,2186
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8530 Å2
ΔGint-120 kcal/mol
Surface area25240 Å2
MethodPISA, PQS
6
G: Periplasmic [NiFe] hydrogenase small subunit
N: Periplasmic [NiFe] hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,2538
Polymers88,0352
Non-polymers1,2186
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8610 Å2
ΔGint-122 kcal/mol
Surface area25500 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)127.500, 99.700, 183.200
Angle α, β, γ (deg.)90.00, 91.80, 90.00
Int Tables number4
Space group name H-MP1211
Number of models2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11N
22G
33G

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
111LYSLYSVALVAL1NL5 - 915 - 91
121LYSLYSLYSLYS3NL9292
131VALVALTYRTYR1NL93 - 27793 - 277
141LYSLYSLYSLYS3NL278278
151ASPASPPROPRO1NL279 - 302279 - 302
161SERSERLYSLYS3NL303 - 304303 - 304
171HISHISVALVAL1NL305 - 327305 - 327
181ASPASPASPASP3NL328328
191LEULEUTYRTYR1NL329 - 341329 - 341
1101ALAALAASPASP6NL342 - 346342 - 346
1111ASPASPTHRTHR1NL346 - 360346 - 360
1121LYSLYSASPASP3NL361 - 366361 - 366
1131HISHISASPASP1NL367 - 405367 - 405
1141METMETLYSLYS3NL406 - 410406 - 410
1151LEULEUILEILE1NL411 - 443411 - 443
1161LYSLYSLYSLYS3NL444 - 452444 - 452
1171ASPASPALAALA1NL453 - 458453 - 458
1181LYSLYSLYSLYS6NL459459
1191TRPTRPPROPRO1NL460 - 527460 - 527
1201LYSLYSARGARG6NL528 - 529528 - 529
1211PROPROHISHIS1NL530 - 549530 - 549
1221FCOFCOMGMG1NVA - UA550 - 553
1231HOHHOHHOHHOH1NHB559 - 586
1241HOHHOHHOHHOH3NHB588 - 589
1251HOHHOHHOHHOH1NHB591 - 599
1261HOHHOHHOHHOH6NHB601 - 602
1271HOHHOHHOHHOH1NHB603 - 671
1281HOHHOHHOHHOH6NHB672
1291HOHHOHHOHHOH1NHB673 - 674
212ALAALAILEILE1GK3 - 813 - 81
222ASPASPASPASP1GK8282
232GLYGLYARGARG1GK83 - 17483 - 174
242SF4SF4SF4SF41GSA267
252HOHHOHHOHHOH1GGB5268 - 5278
262HOHHOHHOHHOH1GGB5280 - 5320
313PROPROLYSLYS2GK175 - 176175 - 176
323LEULEULEULEU3GK177177
333PHEPHEF3SF3S2GK - RA178 - 266178

NCS ensembles :
ID
1
2
3
Detailsheterodimer of small and large subunit

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Components

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Periplasmic [NiFe] hydrogenase ... , 2 types, 12 molecules ABCDFGHIJKMN

#1: Protein
Periplasmic [NiFe] hydrogenase small subunit / NiFe hydrogenlyase small chain


Mass: 28305.279 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Desulfovibrio fructosovorans (bacteria) / Cellular location: periplasm / Strain: wild type / References: UniProt: P18187, cytochrome-c3 hydrogenase
#2: Protein
Periplasmic [NiFe] hydrogenase large subunit / NiFe hydrogenlyase large chain


Mass: 59729.312 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Desulfovibrio fructosovorans (bacteria) / Cellular location: periplasm / Strain: wild type / References: UniProt: P18188, cytochrome-c3 hydrogenase

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Non-polymers , 6 types, 1922 molecules

#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical
ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe3S4
#5: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ni
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


Mass: 135.890 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3FeN2O
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1886 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 293 K / pH: 6.3
Details: PEG 6000, MES buffer, glycerol, Tris-HCL, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.30

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.93
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 14, 2001
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 233855 / % possible obs: 87.5 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 26.3 Å2 / Rsym value: 0.077 / Net I/σ(I): 9.7
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 4.4 / Rsym value: 0.209 / % possible all: 61.9

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Processing

Software
NameVersionClassification
REFMAC5.1.27refinement
ProDCdata collection
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YQW

1yqw


Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.18 / SU ML: 0.159 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.4 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: IN ADDITION TLS PARAMETERS WERE REFINED FOR THE INDIVIDUAL SUBUNITS. FOR ONE OF THE SIX HYDROGENASE HETERODIMERS IN THE ASYMMETRIC UNIT (SEGID G AND N) TWO OVERLAPPING MOLECULAR REPLACEMENT ...Details: IN ADDITION TLS PARAMETERS WERE REFINED FOR THE INDIVIDUAL SUBUNITS. FOR ONE OF THE SIX HYDROGENASE HETERODIMERS IN THE ASYMMETRIC UNIT (SEGID G AND N) TWO OVERLAPPING MOLECULAR REPLACEMENT SOLUTIONS WERE FOUND. DURING REFINEMENT THEIR OCCUPANCIES WERE OPTIMIZED TO 0.59 AND 0.41, RESPECTIVELY. THE FIRST CONFORMER IS INCLUDED, TOGETHER WITH THE FIVE OTHER HYDROGENASE MOLECULES, AS MODEL 1. THE SECOND ONE AS MODEL 2, AGAIN INCLUDING THE FIVE OTHER HYDROGENASE MOLECULES (THESE ARE IDENTICAL TO THE ONES IN MODEL 1). THE TWO CONFORMERS WERE REFINED WITH TIGHT NON- CRYSTALLOGRAPHIC SYMMETRY RESTRAINTS (SEE REMARK 3) OTHER REFINEMENT REMARKS For Model 2, TlS groups 1-10 are the same as for Model 1. Chains N and G are different in Model 2 according to below: TLS GROUP : 11 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : G 3 G 264 RESIDUE RANGE : G 265 G 267 RESIDUE RANGE : 5268 5322 ORIGIN FOR THE GROUP (A): 131.4780 -38.2890 38.8970 T TENSOR T11: 0.2569 T22: 0.2308 T33: 0.4163 T12: 0.0494 T13: 0.2805 T23: -0.0375 L TENSOR L11: 1.3547 L22: 1.7758 L33: 3.2247 L12: -0.2851 L13: 0.1621 L23: 0.3422 S TENSOR S11: 0.0326 S12: 0.0717 S13: -0.1022 S21: 0.0655 S22: -0.0055 S23: -0.0258 S31: 0.2899 S32: 0.4537 S33: -0.0271 TLS GROUP : 12 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : N 5 N 549 RESIDUE RANGE : N 550 N 553 RESIDUE RANGE : 5554 5679 ORIGIN FOR THE GROUP (A): 112.1110 -24.7590 42.5650 T TENSOR T11: 0.3226 T22: 0.1431 T33: 0.4052 T12: 0.0067 T13: 0.2573 T23: -0.0306 L TENSOR L11: 0.5751 L22: 0.8994 L33: 2.1004 L12: 0.0846 L13: -0.3204 L23: -0.2637 S TENSOR S11: 0.0046 S12: 0.0836 S13: 0.0156 S21: -0.1287 S22: 0.0811 S23: -0.0461 S31: -0.1311 S32: -0.1867 S33: -0.0857
RfactorNum. reflection% reflectionSelection details
Rfree0.22 11803 5.1 %RANDOM
Rwork0.171 ---
obs0.173 233638 87.6 %-
all-233638 --
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: 9.98 Å2
Baniso -1Baniso -2Baniso -3
1-3 Å20 Å21.21 Å2
2---1.01 Å20 Å2
3----1.91 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms36776 0 192 1886 38854
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02144467
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3391.95960329
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3255629
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0760.26541
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0233598
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2350.219586
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.22470
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3230.2121
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2460.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.151.528086
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.666245028
X-RAY DIFFRACTIONr_scbond_it2.076216381
X-RAY DIFFRACTIONr_scangle_it2.846315112
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
11N4154tight positional0.020.02
22G1309tight positional0.020.02
33G360tight positional0.010.02
33G371medium positional0.130.2
11N146loose positional0.775
33G4loose positional0.95
11N4154tight thermal0.080.5
22G1309tight thermal0.070.5
33G360tight thermal0.060.5
33G371medium thermal0.673
11N146loose thermal1.4410
33G4loose thermal1.1410
LS refinement shellResolution: 2.1→2.19 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.258 1100 -
Rwork0.207 19841 -
obs--65.1 %
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)
11.25130.3794-0.38661.4145-0.03981.07670.0771-0.09830.201-0.0172-0.04340.2146-0.2371-0.0398-0.03370.0923-0.0119-0.02340.1025-0.05210.176516.13523.00185.889
20.72450.1041-0.12620.9762-0.01510.8537-0.043-0.0127-0.0699-0.16280.02610.05550.0633-0.03120.01690.0552-0.0161-0.04210.0977-0.01140.141520.3911.54276.124
30.97290.1188-0.14450.76710.09861.8021-0.12610.021-0.2473-0.1079-0.0244-0.17570.44940.27850.15050.2220.06070.05750.1953-0.01520.297967.521-38.08338.713
40.76410.1139-0.2540.7693-0.24171.4316-0.11360.1085-0.065-0.08560.04510.0330.1375-0.17710.06850.0806-0.0353-0.0420.151-0.03270.149848.075-24.58842.328
50.7509-0.2325-0.37451.58980.35541.91160.04660.0252-0.06240.0529-0.0672-0.18620.16460.25280.02050.07430.0047-0.08270.15490.02990.131145.80914.1229.866
60.7814-0.0895-0.15371.36850.0521.30180.11560.21590.0626-0.2199-0.14840.0222-0.1115-0.03870.03280.10350.0441-0.07330.17510.01520.13534.32827.18513.405
71.05830.1524-0.6320.64770.06351.66160.02160.00740.1204-0.060.02190.0419-0.1185-0.0152-0.04350.03070.0038-0.06380.0597-0.00650.132580.80322.84386.841
80.59120.1322-0.19280.7388-0.16851.3864-0.07220.0382-0.0509-0.14760.03090.02280.38960.02820.04130.15780.0044-0.040.0725-0.01170.119785.2481.53477.031
91.0073-0.0931-1.02370.87170.24952.4429-0.005-0.145-0.05940.020.0575-0.13520.30990.3701-0.05250.13630.0309-0.05270.1813-0.0150.1567110.39714.54230.492
101.1028-0.1552-0.77940.8310.2441.92880.230.30490.1686-0.1506-0.0530.0127-0.1808-0.2861-0.1770.11290.0364-0.01730.19690.02040.193398.20926.79514.006
111.64960.53920.06321.38540.90861.53580.03720.0414-0.67950.09760.1357-0.53040.42170.2762-0.1730.1825-0.0033-0.05690.2174-0.10220.5799129.524-40.12436.978
122.10511.17840.51161.92040.60810.935-0.0974-0.0165-0.1321-0.04170.0948-0.0397-0.0214-0.15670.00260.0774-0.0509-0.05050.1518-0.01330.1014112.159-24.55742.201
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 2643 - 264
2X-RAY DIFFRACTION1AY - AA265 - 2671
3X-RAY DIFFRACTION1AWA268 - 3921 - 120
4X-RAY DIFFRACTION2HB5 - 5495 - 549
5X-RAY DIFFRACTION2HBA - S550 - 5531
6X-RAY DIFFRACTION2HCB554 - 7921 - 339
7X-RAY DIFFRACTION3BC3 - 2643 - 264
8X-RAY DIFFRACTION3BCA - EA265 - 2671
9X-RAY DIFFRACTION3BXA1268 - 13471 - 72
10X-RAY DIFFRACTION4ID5 - 5495 - 549
11X-RAY DIFFRACTION4IFA - T550 - 5531
12X-RAY DIFFRACTION4IDB565 - 77112 - 218
13X-RAY DIFFRACTION5CE5 - 2645 - 264
14X-RAY DIFFRACTION5CGA - IA265 - 2671
15X-RAY DIFFRACTION5CYA2268 - 23863 - 114
16X-RAY DIFFRACTION6JF6 - 5496 - 549
17X-RAY DIFFRACTION6JJA - U550 - 5531
18X-RAY DIFFRACTION6JEB565 - 76012 - 207
19X-RAY DIFFRACTION7DG3 - 2643 - 264
20X-RAY DIFFRACTION7DKA - MA265 - 2671
21X-RAY DIFFRACTION7DZA3268 - 342296 - 148
22X-RAY DIFFRACTION8KH6 - 5496 - 549
23X-RAY DIFFRACTION8KNA - V550 - 5531
24X-RAY DIFFRACTION8KFB566 - 80613 - 253
25X-RAY DIFFRACTION9FI5 - 2645 - 264
26X-RAY DIFFRACTION9FOA - QA265 - 2671
27X-RAY DIFFRACTION9FAB4270 - 43821 - 105
28X-RAY DIFFRACTION10MJ5 - 5495 - 549
29X-RAY DIFFRACTION10MRA - W550 - 5531
30X-RAY DIFFRACTION10MGB568 - 73615 - 183
31X-RAY DIFFRACTION11GK3 - 2643 - 264
32X-RAY DIFFRACTION11GSA - UA265 - 2671
33X-RAY DIFFRACTION11GBB5268 - 53221 - 53
34X-RAY DIFFRACTION12NL5 - 5495 - 549
35X-RAY DIFFRACTION12NVA - X550 - 5531
36X-RAY DIFFRACTION12NHB559 - 6916 - 138

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