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- PDB-3rq6: Crystal Structure of ADP/ATP-dependent NAD(P)H-hydrate dehydratas... -

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Basic information

Entry
Database: PDB / ID: 3rq6
TitleCrystal Structure of ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Bacillus subtilis soaked with ADP-ribose
ComponentsADP/ATP-dependent NAD(P)H-hydrate dehydratase
Keywordslyase/lyase substrate / STRUCTURAL GENOMICS / PSI-biology / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG / LYASE / lyase-lyase substrate complex
Function / homology
Function and homology information


metabolite repair / ADP-dependent NAD(P)H-hydrate dehydratase / ADP-dependent NAD(P)H-hydrate dehydratase activity / NADHX epimerase activity / NADPHX epimerase activity / nicotinamide nucleotide metabolic process / ATP binding
Similarity search - Function
YjeF C-terminal domain signature 1. / Carbohydrate kinase, predicted, conserved site / YjeF C-terminal domain signature 2. / ATP/ADP-dependent (S)-NAD(P)H-hydrate dehydratase / Carbohydrate kinase / YjeF C-terminal domain profile. / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5-DIPHOSPHORIBOSE / ADP-dependent (S)-NAD(P)H-hydrate dehydratase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsShumilin, I.A. / Cymborowski, M. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Structure / Year: 2012
Title: Identification of unknown protein function using metabolite cocktail screening.
Authors: Shumilin, I.A. / Cymborowski, M. / Chertihin, O. / Jha, K.N. / Herr, J.C. / Lesley, S.A. / Joachimiak, A. / Minor, W.
History
DepositionApr 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2011Group: Structure summary
Revision 1.2Jan 9, 2013Group: Database references
Revision 1.3Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 13, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADP/ATP-dependent NAD(P)H-hydrate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3194
Polymers30,1761
Non-polymers1,1433
Water3,459192
1
A: ADP/ATP-dependent NAD(P)H-hydrate dehydratase
hetero molecules

A: ADP/ATP-dependent NAD(P)H-hydrate dehydratase
hetero molecules

A: ADP/ATP-dependent NAD(P)H-hydrate dehydratase
hetero molecules

A: ADP/ATP-dependent NAD(P)H-hydrate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,27816
Polymers120,7064
Non-polymers4,57212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area18290 Å2
ΔGint-105 kcal/mol
Surface area36380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.542, 91.542, 169.131
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-343-

HOH

21A-387-

HOH

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Components

#1: Protein ADP/ATP-dependent NAD(P)H-hydrate dehydratase


Mass: 30176.439 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSU38720, yxkO / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIPL
References: UniProt: P94368, ATP-dependent NAD(P)H-hydrate dehydratase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O

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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: 2.94 Å3/Da / Density % sol: 58.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.18 M Magnesium Cloride, 19%(v/v) PEG 400, 10%(v/v) Glycerol, 0.09 M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 16, 2009 / Details: MIRRORS
Diffraction measurementDetails: 1.00 degrees, 1.00 sec, detector distance 150.00 mm
Method: scans
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionAv R equivalents: 0.056 / Number: 454329
ReflectionResolution: 1.65→50 Å / Num. obs: 43866 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.4 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 44.969
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.833 / Mean I/σ(I) obs: 1.984 / Rsym value: 0.833 / % possible all: 100
Cell measurementReflection used: 454329

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.006data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KYH
Resolution: 1.65→50 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 2.703 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.176 2188 5 %RANDOM
Rwork0.15 ---
obs0.151 43423 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 85.74 Å2 / Biso mean: 30.92 Å2 / Biso min: 18.99 Å2
Baniso -1Baniso -2Baniso -3
1--1.29 Å20 Å20 Å2
2---1.29 Å20 Å2
3---2.59 Å2
Refinement stepCycle: LAST / Resolution: 1.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2107 0 64 192 2363
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222258
X-RAY DIFFRACTIONr_bond_other_d00.021478
X-RAY DIFFRACTIONr_angle_refined_deg1.7981.9953099
X-RAY DIFFRACTIONr_angle_other_deg4.21733628
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5795284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.48724.17691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.86515350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3911512
X-RAY DIFFRACTIONr_chiral_restr0.120.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212487
X-RAY DIFFRACTIONr_gen_planes_other0.0150.02428
X-RAY DIFFRACTIONr_mcbond_it1.0351.51389
X-RAY DIFFRACTIONr_mcbond_other01.5565
X-RAY DIFFRACTIONr_mcangle_it1.76722232
X-RAY DIFFRACTIONr_scbond_it2.8063869
X-RAY DIFFRACTIONr_scangle_it4.5054.5863
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.205 163 -
Rwork0.197 3036 -
all-3199 -
obs--100 %
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)
14.70164.6822-2.35365.9005-2.10471.64830.0275-0.2421-0.16840.2129-0.1235-0.14780.03590.05380.0960.21280.01480.00940.15540.05480.035949.57815.89939.399
20.76530.37630.07851.37930.08660.7796-0.03790.068-0.0511-0.13250.0101-0.05930.10990.08690.02780.15440.01420.020.12950.00510.011151.23824.18714.8
30.4704-0.3344-0.0010.9041-0.05230.4629-0.0252-0.0442-0.10470.0653-0.00360.09610.1195-0.04790.02880.1608-0.0130.02650.10780.01680.037439.91217.92428.501
44.6768-0.8551.18451.6697-0.60323.8109-0.0904-0.2339-0.07090.35210.07220.08290.064-0.18150.01820.1794-0.0110.01640.16680.02260.011549.98530.28138.396
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 19
2X-RAY DIFFRACTION2A20 - 145
3X-RAY DIFFRACTION3A146 - 264
4X-RAY DIFFRACTION4A265 - 276

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