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- PDB-2woe: Crystal Structure of the D97N variant of dinitrogenase reductase-... -

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Basic information

Entry
Database: PDB / ID: 2woe
TitleCrystal Structure of the D97N variant of dinitrogenase reductase- activating glycohydrolase (DRAG) from Rhodospirillum rubrum in complex with ADP-ribose
ComponentsADP-RIBOSYL-[DINITROGEN REDUCTASE] GLYCOHYDROLASE
KeywordsHYDROLASE / DIMANGANESE / NITROGEN FIXATION / ADP-RIBOSYLGLYCOHYDROLASE / MONO-ADP-RIBOSYLHYDROLASE
Function / homology
Function and homology information


ADP-ribosyl-[dinitrogen reductase] hydrolase / ADP-ribosyl-[dinitrogen reductase] hydrolase activity / protein de-ADP-ribosylation / nitrogen fixation / metal ion binding / cytoplasm
Similarity search - Function
ADP-ribosyl-dinitrogen reductase hydrolase / ADP-ribosylglycohydrolase fold / ADP-ribosylation/Crystallin J1 / ADP-ribosylation/Crystallin J1 / ADP-ribosylglycohydrolase / ADP-ribosylation/Crystallin J1 superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-AR6 / : / L(+)-TARTARIC ACID / ADP-ribosyl-[dinitrogen reductase] glycohydrolase
Similarity search - Component
Biological speciesRHODOSPIRILLUM RUBRUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBerthold, C.L. / Wang, H. / Nordlund, S. / Hogbom, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Mechanism of Adp-Ribosylation Removal Revealed by the Structure and Ligand Complexes of the Dimanganese Mono-Adp-Ribosylhydrolase Drag.
Authors: Berthold, C.L. / Wang, H. / Nordlund, S. / Hogbom, M.
History
DepositionJul 23, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADP-RIBOSYL-[DINITROGEN REDUCTASE] GLYCOHYDROLASE
B: ADP-RIBOSYL-[DINITROGEN REDUCTASE] GLYCOHYDROLASE
C: ADP-RIBOSYL-[DINITROGEN REDUCTASE] GLYCOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,81611
Polymers96,7313
Non-polymers2,0858
Water13,655758
1
A: ADP-RIBOSYL-[DINITROGEN REDUCTASE] GLYCOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1005
Polymers32,2441
Non-polymers8564
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ADP-RIBOSYL-[DINITROGEN REDUCTASE] GLYCOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8583
Polymers32,2441
Non-polymers6142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ADP-RIBOSYL-[DINITROGEN REDUCTASE] GLYCOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8583
Polymers32,2441
Non-polymers6142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.110, 84.360, 146.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 3 - 293 / Label seq-ID: 8 - 298

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

NCS oper:
IDCodeMatrixVector
1given(-0.793, -0.291, -0.535), (0.468, 0.27, -0.841), (0.389, -0.918, -0.078)-61.05373, -4.64983, 23.38663
2given(-0.375, 0.583, 0.72), (-0.533, 0.5, -0.683), (-0.758, -0.64, 0.123)-44.23806, -27.99249, -18.81052

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein ADP-RIBOSYL-[DINITROGEN REDUCTASE] GLYCOHYDROLASE / DINITROGENASE REDUCTASE-ACTIVATING GLYCOHYDROLAS / EADP-RIBOSYLGLYCOHYDROLASE


Mass: 32243.768 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOSPIRILLUM RUBRUM (bacteria) / Strain: S1 / Plasmid: PGEX-6P-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 STAR (DE3)
References: UniProt: P14300, ADP-ribosyl-[dinitrogen reductase] hydrolase

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Non-polymers , 5 types, 766 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#4: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 758 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 97 TO ASN ENGINEERED RESIDUE IN CHAIN B, ASP 97 TO ASN ...ENGINEERED RESIDUE IN CHAIN A, ASP 97 TO ASN ENGINEERED RESIDUE IN CHAIN B, ASP 97 TO ASN ENGINEERED RESIDUE IN CHAIN C, ASP 97 TO ASN

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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: 2.4 Å3/Da / Density % sol: 48 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→73.13 Å / Num. obs: 78445 / % possible obs: 97.8 % / Observed criterion σ(I): 3 / Redundancy: 4.4 % / Biso Wilson estimate: 22.4 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.3
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.7 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 6.241 / SU ML: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20731 3955 5 %RANDOM
Rwork0.1671 ---
obs0.16912 74423 97.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.657 Å2
Baniso -1Baniso -2Baniso -3
1-1.86 Å20 Å20 Å2
2---2.05 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6612 0 127 758 7497
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0216929
X-RAY DIFFRACTIONr_bond_other_d0.0010.024626
X-RAY DIFFRACTIONr_angle_refined_deg1.1981.9759414
X-RAY DIFFRACTIONr_angle_other_deg0.919311235
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1535888
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.93622.881295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.261151117
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1421558
X-RAY DIFFRACTIONr_chiral_restr0.0650.21051
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027773
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021434
X-RAY DIFFRACTIONr_nbd_refined0.2020.21633
X-RAY DIFFRACTIONr_nbd_other0.1820.24991
X-RAY DIFFRACTIONr_nbtor_refined0.1710.23485
X-RAY DIFFRACTIONr_nbtor_other0.0840.23351
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2584
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2410.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1080.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5941.55630
X-RAY DIFFRACTIONr_mcbond_other0.1241.51821
X-RAY DIFFRACTIONr_mcangle_it0.65326864
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.39732995
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1324.52541
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

Ens-ID: 1 / Number: 3636 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.390.5
2Bmedium positional0.350.5
3Cmedium positional0.350.5
1Amedium thermal0.432
2Bmedium thermal0.472
3Cmedium thermal0.382
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 304 -
Rwork0.25 5439 -
obs--97.95 %
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)
11.2132-0.26870.10551.8651-0.55371.72940.01750.09910.0819-0.1476-0.005-0.01950.02950.0768-0.0125-0.1781-0.0017-0.0195-0.1570.0098-0.1316-12.3738-4.42319.2048
20.79480.144-0.18351.9819-0.17421.5170.0071-0.00510.02480.0437-0.04220.0221-0.1619-0.01070.0352-0.1327-0.00610.0112-0.16150.0059-0.1601-44.0344-1.0638-25.1247
31.9908-0.42180.24292.2106-0.06071.7390.0159-0.17480.00480.09210.01070.0625-0.04270.002-0.0266-0.1537-0.0084-0.0012-0.12160.0273-0.1177-45.76412.438110.3156
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 293
2X-RAY DIFFRACTION2B3 - 293
3X-RAY DIFFRACTION3C3 - 293

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