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- PDB-2wod: Crystal Structure of the dinitrogenase reductase-activating glyco... -

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Basic information

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


ADP-ribosyl-[dinitrogen reductase] hydrolase / protein de-ADP-ribosylation / ADP-ribosyl-[dinitrogen reductase] hydrolase activity / 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-ZZC / ADP-ribosyl-[dinitrogen reductase] glycohydrolase
Similarity search - Component
Biological speciesRHODOSPIRILLUM RUBRUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_entry_details.has_protein_modification / _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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9029
Polymers64,4902
Non-polymers1,4127
Water4,486249
1
A: ADP-RIBOSYL-[DINITROGEN REDUCTASE] GLYCOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8413
Polymers32,2451
Non-polymers5962
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)33,0616
Polymers32,2451
Non-polymers8165
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.306, 77.306, 245.593
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.356, -0.933, -0.055), (0.918, -0.36, 0.167), (-0.176, 0.009, 0.984)
Vector: 60.48688, -57.10409, -3.983)

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 32244.752 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: LYS B54 IS MONO-ADP-RIBOSYLATED / Source: (gene. exp.) RHODOSPIRILLUM RUBRUM (bacteria) / Strain: S1 / Plasmid: PGEX-6P-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) STAR
References: UniProt: P14300, ADP-ribosyl-[dinitrogen reductase] hydrolase

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Non-polymers , 5 types, 256 molecules

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


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-ZZC / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [[(2R,3R)-2,3-DIHYDROXY-4-OXO-PENTOXY]-OXIDO-PHOSPHORYL] PHOSPHATE


Mass: 541.300 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H21N5O13P2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer details1'-DEOXY ADP-RIBOSYL (ZZC): C1' IS COVALENTLY LINKED TO THE EPSILON-AMINO GROUP OF LYS54

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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: 3.2 Å3/Da / Density % sol: 61 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.99
DetectorDate: Sep 11, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.2→36.86 Å / Num. obs: 43703 / % possible obs: 99.2 % / Observed criterion σ(I): 3 / Redundancy: 3.1 % / Biso Wilson estimate: 36.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.6
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.1 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→34.92 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / SU B: 13.081 / SU ML: 0.169 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.222 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE ADP-RIBSOYLLYSINE KETOAMINE AT RESIDUE B54 REACHES INTO THE ACTIVE SITE OF THE CHAIN A SUBUNIT
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2082 5.1 %RANDOM
Rwork0.197 ---
obs0.199 38837 98.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.532 Å2
Baniso -1Baniso -2Baniso -3
1-3.36 Å21.68 Å20 Å2
2--3.36 Å20 Å2
3----5.04 Å2
Refinement stepCycle: LAST / Resolution: 2.25→34.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4408 0 85 249 4742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0214596
X-RAY DIFFRACTIONr_bond_other_d0.0010.023071
X-RAY DIFFRACTIONr_angle_refined_deg1.1831.9736231
X-RAY DIFFRACTIONr_angle_other_deg1.55237449
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1475584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.91122.872195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.9215740
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3761538
X-RAY DIFFRACTIONr_chiral_restr0.0590.2690
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025146
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02944
X-RAY DIFFRACTIONr_nbd_refined0.1970.21136
X-RAY DIFFRACTIONr_nbd_other0.1790.23286
X-RAY DIFFRACTIONr_nbtor_refined0.170.22282
X-RAY DIFFRACTIONr_nbtor_other0.0860.22252
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2219
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1970.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0970.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.471.53728
X-RAY DIFFRACTIONr_mcbond_other0.0761.51210
X-RAY DIFFRACTIONr_mcangle_it0.56924552
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.10231985
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.6594.51677
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
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 139 -
Rwork0.273 2831 -
obs--99.23 %
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)
11.0780.4351-0.4262.3571-0.53244.4203-0.04-0.0713-0.2535-0.2434-0.0529-0.24330.54580.10840.09290.15430.03110.0449-0.24950.0191-0.10936.2581-24.4663-25.0573
21.41560.70280.43422.06240.1173.4575-0.0088-0.1520.0199-0.1467-0.0557-0.0066-0.08250.12930.0645-0.1326-0.0309-0.0094-0.2167-0.0134-0.172242.281510.6576-13.9611
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 293
2X-RAY DIFFRACTION2B3 - 293

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