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- PDB-1h0h: Tungsten containing Formate Dehydrogenase from Desulfovibrio Gigas -

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Basic information

Entry
Database: PDB / ID: 1h0h
TitleTungsten containing Formate Dehydrogenase from Desulfovibrio Gigas
Components(FORMATE DEHYDROGENASE SUBUNIT ...) x 2
KeywordsELECTRON TRANSPORT / TUNGSTEN SELENIUM FORMATE DEHYDROGENASE / SELENOCYSTEINE / MOLYBDOPTERIN / MGD / IRON-SULPHUR CLUSTER / PERIPLASMIC
Function / homology
Function and homology information


formate dehydrogenase (cytochrome-c-553) activity / formate dehydrogenase / formate dehydrogenase (NAD+) activity / molybdopterin cofactor binding / cellular respiration / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / metal ion binding
Similarity search - Function
Formate dehydrogenase-N, alpha subunit / : / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 / Rossmann fold - #740 / 4Fe-4S dicluster domain / Molybdopterin oxidoreductase, molybdopterin cofactor binding site / Prokaryotic molybdopterin oxidoreductases signature 1. / Prokaryotic molybdopterin oxidoreductases signature 3. / Molybdopterin oxidoreductase, prokaryotic, conserved site ...Formate dehydrogenase-N, alpha subunit / : / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 / Rossmann fold - #740 / 4Fe-4S dicluster domain / Molybdopterin oxidoreductase, molybdopterin cofactor binding site / Prokaryotic molybdopterin oxidoreductases signature 1. / Prokaryotic molybdopterin oxidoreductases signature 3. / Molybdopterin oxidoreductase, prokaryotic, conserved site / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Alpha-Beta Plaits - #20 / Barwin-like endoglucanases - #20 / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Barwin-like endoglucanases / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Alpha-Beta Plaits / Beta Barrel / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANYLATE-O'-PHOSPHORIC ACID / Chem-MGD / IRON/SULFUR CLUSTER / : / Formate dehydrogenase subunit beta / Formate dehydrogenase subunit alpha
Similarity search - Component
Biological speciesDESULFOVIBRIO GIGAS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRaaijmakers, H.C.A.
Citation
Journal: Structure / Year: 2002
Title: Gene Sequence and the 1.8 A Crystal Structure of the Tungsten-Containing Formate Dehydrogenase from Desulfovibrio Gigas
Authors: Raaijmakers, H.C.A. / Macieira, S. / Dias, J. / Teixeira, S. / Bursakov, S. / Huber, R. / Moura, J. / Moura, I. / Romao, M.
#1: Journal: J.Biol.Inorg.Chem. / Year: 2001
Title: Tungsten-Containing Formate Dehydrogenase from Desulfovibrio Gigas: Metal Identification and Preliminary Structural Data by Multi-Wavelength Crystallography
Authors: Raaijmakers, H. / Teixeira, S. / Dias, J.M. / Almendra, M.J. / Brondino, C.D. / Moura, I. / Moura, J. / Romao, M.J.
History
DepositionJun 19, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2003Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Jun 28, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jan 23, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / database_PDB_caveat ...atom_site / database_PDB_caveat / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.ptnr1_label_atom_id
Revision 2.1Apr 3, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 2.2May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 2.3Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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_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.pdbx_dist_value / _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_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AL" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AL" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "KL" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FORMATE DEHYDROGENASE SUBUNIT ALPHA
B: FORMATE DEHYDROGENASE SUBUNIT BETA
K: FORMATE DEHYDROGENASE SUBUNIT ALPHA
L: FORMATE DEHYDROGENASE SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)274,26824
Polymers267,5644
Non-polymers6,70420
Water30,7701708
1
A: FORMATE DEHYDROGENASE SUBUNIT ALPHA
B: FORMATE DEHYDROGENASE SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,13412
Polymers133,7822
Non-polymers3,35210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8690 Å2
ΔGint-147.1 kcal/mol
Surface area38290 Å2
MethodPISA
2
K: FORMATE DEHYDROGENASE SUBUNIT ALPHA
L: FORMATE DEHYDROGENASE SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,13412
Polymers133,7822
Non-polymers3,35210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8640 Å2
ΔGint-148.9 kcal/mol
Surface area38390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.408, 110.398, 156.185
Angle α, β, γ (deg.)90.00, 93.53, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21K
12B
22L

NCS domain segments:

Refine code: 2

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETASNASNAA3 - 663 - 66
211METMETASNASNKC3 - 663 - 66
121ARGARGALAALAAA68 - 9668 - 96
221ARGARGALAALAKC68 - 9668 - 96
131ARGARGLYSLYSAA98 - 28998 - 289
231ARGARGLYSLYSKC98 - 28998 - 289
141TYRTYRASPASPAA294 - 304294 - 304
241TYRTYRASPASPKC294 - 304294 - 304
151ASNASNTHRTHRAA306 - 366306 - 366
251ASNASNTHRTHRKC306 - 366306 - 366
161GLYGLYTYRTYRAA372 - 439372 - 439
261GLYGLYTYRTYRKC372 - 439372 - 439
171GLUGLUASNASNAA441 - 480441 - 480
271GLUGLUASNASNKC441 - 480441 - 480
181ALAALATRPTRPAA482 - 497482 - 497
281ALAALATRPTRPKC482 - 497482 - 497
191THRTHRPHEPHEAA499 - 505499 - 505
291THRTHRPHEPHEKC499 - 505499 - 505
1101GLYGLYARGARGAA507 - 530507 - 530
2101GLYGLYARGARGKC507 - 530507 - 530
1111ALAALALYSLYSAA532 - 561532 - 561
2111ALAALALYSLYSKC532 - 561532 - 561
1121ILEILELEULEUAA563 - 660563 - 660
2121ILEILELEULEUKC563 - 660563 - 660
1131ASPASPGLYGLYAA662 - 666662 - 666
2131ASPASPGLYGLYKC662 - 666662 - 666
1141VALVALALAALAAA668 - 762668 - 762
2141VALVALALAALAKC668 - 762668 - 762
1151LYSLYSASPASPAA765 - 780765 - 780
2151LYSLYSASPASPKC765 - 780765 - 780
1161GLUGLUARGARGAA782 - 803782 - 803
2161GLUGLUARGARGKC782 - 803782 - 803
1171ASPASPPHEPHEAA805 - 836805 - 836
2171ASPASPPHEPHEKC805 - 836805 - 836
1181ARGARGPROPROAA847 - 955847 - 955
2181ARGARGPROPROKC847 - 955847 - 955
1191LYSLYSALAALAAA968 - 977968 - 977
2191LYSLYSALAALAKC968 - 977968 - 977
112SERSERPHEPHEBB1 - 671 - 67
212SERSERPHEPHELD1 - 671 - 67
122PROPROALAALABB69 - 17869 - 178
222PROPROALAALALD69 - 17869 - 178
132ILEILEALAALABB180 - 214180 - 214
232ILEILEALAALALD180 - 214180 - 214

NCS ensembles :
ID
1
2

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Components

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FORMATE DEHYDROGENASE SUBUNIT ... , 2 types, 4 molecules AKBL

#1: Protein FORMATE DEHYDROGENASE SUBUNIT ALPHA / FDH SUBUNIT ALPHA / FORMATE DEHYDROGENASE LARGE SUBUNIT


Mass: 109900.859 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: NATIVE PROTEIN / Source: (natural) DESULFOVIBRIO GIGAS (bacteria) / Strain: NCIB 9332 / References: UniProt: Q934F5, formate dehydrogenase
#2: Protein FORMATE DEHYDROGENASE SUBUNIT BETA / FDH SUBUNIT BETA / FORMATE DEHYDROGENASE SMALL SUBUNIT


Mass: 23881.049 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO GIGAS (bacteria) / Strain: NCIB 9332 / References: UniProt: Q8GC87

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Non-polymers , 8 types, 1728 molecules

#3: Chemical ChemComp-W / TUNGSTEN ION


Mass: 183.840 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: W
#4: Chemical ChemComp-2MD / GUANYLATE-O'-PHOSPHORIC ACID MONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,5,6,7,8A,9,10,10A-OCTAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL) ESTER / MOLYBDENUM COFACTOR,BIS (MOLYBDOPTERIN GUANINE DINUCLEOTIDE)


Mass: 742.573 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28N10O13P2S2
#5: Chemical ChemComp-MGD / 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE / MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE


Mass: 740.557 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2
#6: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
#7: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe4S4
#8: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#9: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1708 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsTHE RESIDUES A1003 AND K1003 WERE ORIGINALLY DEPOSITED AS ISOLATED SULFUR ATOMS. AS PART OF ...THE RESIDUES A1003 AND K1003 WERE ORIGINALLY DEPOSITED AS ISOLATED SULFUR ATOMS. AS PART OF REMEDIATION, THESE HAVE HAVE BEEN CHANGED TO UNX (UNKNOWN ATOM OR LIGAND) AS THE HETEROGEN S IS NOW OBSOLETE IN THE PDB HETGROUP DICTIONARY.
Sequence detailsFORMATE DEHYDROGENASE SMALL SUBUNIT SEQUENCE IS ON HOLD, ACCESSION NUMBER P83237

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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: 54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES 7.5, 20% PEG 3350 (W/V), 10% ISOPROPANOL (V/V), 1% BETA-OCTYLGLUCOSIDE, 4 DEGREES CELCIUS, HANGING DROPS., pH 7.50
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop / Details: used macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 MHEPES1droppH7.5
220 %(w/v)PEG33501drop
310 %(v/v)isopropanol1drop
41 %beta-octylglucoside1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.992,1.214,1.735,1.7415
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 15, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9921
21.2141
31.7351
41.74151
ReflectionResolution: 1.8→35 Å / Num. obs: 220129 / % possible obs: 92 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 5
Reflection shellResolution: 1.8→1.88 Å / Redundancy: 1.65 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2 / % possible all: 70
Reflection
*PLUS
Lowest resolution: 35 Å / Num. obs: 10979 / Num. measured all: 208782

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Processing

Software
NameVersionClassification
Omodel building
SCALEPACKdata scaling
SHARPphasing
AMoREphasing
ARP/wARPphasing
Ophasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NAP

2nap


Resolution: 1.8→35 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.831 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.118
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: ATOMS WITH AN OCCUPANCY LESS THAN 1.0 (PARTIALLY) DISORDERED. RESIDUES 1-2, 837-843 AND 956-966 OF T SUBUNIT ARE POORLY DEFINED IN THE ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.201 10979 5 %RANDOM
Rwork0.167 ---
obs0.169 208782 95.7 %-
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: 19.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20.38 Å2
2--1.22 Å20 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.8→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18786 0 288 1708 20782
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02219963
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.99427119
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.49532419
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.862153543
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1070.22819
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215185
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.310190
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.52231
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2990.389
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2440.542
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.97211981
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.502319363
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.33627982
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.88937689
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 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3901tight positional0.070.04
2B5544tight positional0.050.04
1A3449medium positional0.150.2
2B3449medium positional0.010.2
1A3901tight thermal0.83
2B5544tight thermal1.083
1A3449medium thermal15
2B3449medium thermal1.355
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.326 707
Rwork0.297 13425
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)
10.41670.11180.01690.22270.02410.328-0.0143-0.05590.06940.0493-0.01630.0471-0.0497-0.03070.03060.03440.01020.00020.0131-0.00990.03997.7183-2.015564.8259
20.4898-0.0925-0.10430.2506-0.05680.4927-0.00410.05660.0327-0.0546-0.0271-0.0418-0.04010.04670.03120.0411-0.0165-0.00430.0523-0.00180.04724.739852.130513.1873
30.8277-0.2438-0.27980.98470.2491.2020.00660.1527-0.0297-0.1603-0.0460.04190.001-0.12020.03940.07940.0005-0.00430.03960.00250.00317.8265-3.788426.6974
40.69860.1497-0.12541.0292-0.19541.624-0.0027-0.0462-0.03750.0886-0.01350.0044-0.00690.15480.01620.0396-0.0155-0.0090.0292-0.00850.008214.059753.086851.1508
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 977
2X-RAY DIFFRACTION1A1000 - 1010
3X-RAY DIFFRACTION1A1100
4X-RAY DIFFRACTION2K1 - 977
5X-RAY DIFFRACTION2K1000 - 1010
6X-RAY DIFFRACTION2K1100
7X-RAY DIFFRACTION3B1 - 214
8X-RAY DIFFRACTION3B1011 - 1013
9X-RAY DIFFRACTION4L1 - 214
10X-RAY DIFFRACTION4L1011 - 1013
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 35 Å / Rfactor Rfree: 0.213 / 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_deg1.792

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