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- PDB-3rq5: Crystal Structure of ADP/ATP-dependent NAD(P)H-hydrate dehydratas... -

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Basic information

Entry
Database: PDB / ID: 3rq5
TitleCrystal Structure of ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Bacillus subtilis co-crystallized with ATP/Mg2+ and soaked with CoA
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


ADP-dependent NAD(P)H-hydrate dehydratase / ADP-dependent NAD(P)H-hydrate dehydratase activity / NAD(P)HX epimerase activity / metabolite repair / 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 / NAD(P)H-hydrate dehydratase / 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
COENZYME A / ADP-dependent (S)-NAD(P)H-hydrate dehydratase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 / 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 / _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

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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)31,1284
Polymers30,1761
Non-polymers9523
Water3,045169
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)124,51316
Polymers120,7064
Non-polymers3,80712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-y-1,x,z1
crystal symmetry operation4_545y,-x-1,z1
Buried area14590 Å2
ΔGint-55 kcal/mol
Surface area36930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.765, 91.765, 169.498
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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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-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.96 Å3/Da / Density % sol: 58.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.005 M ATP, 0.18 M Magnesium Cloride, 13.5%(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, 2.50 sec, detector distance 160.00 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: 384069
ReflectionResolution: 1.7→50 Å / Num. obs: 40558 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.5 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 38.846
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.488 / Rsym value: 0.61 / % possible all: 100
Cell measurementReflection used: 384069

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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

1kyh


Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.719 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.178 2007 5 %RANDOM
Rwork0.153 ---
obs0.154 40127 99.95 %-
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: 64.42 Å2 / Biso mean: 27.387 Å2 / Biso min: 15.87 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å20 Å20 Å2
2---1.1 Å20 Å2
3---2.19 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 43 169 2271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222152
X-RAY DIFFRACTIONr_bond_other_d00.021414
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.9882940
X-RAY DIFFRACTIONr_angle_other_deg4.18333467
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.255268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.36924.23585
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.68715335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2231511
X-RAY DIFFRACTIONr_chiral_restr0.0940.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212357
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02396
X-RAY DIFFRACTIONr_mcbond_it0.891.51342
X-RAY DIFFRACTIONr_mcbond_other01.5546
X-RAY DIFFRACTIONr_mcangle_it1.6222154
X-RAY DIFFRACTIONr_scbond_it2.6583810
X-RAY DIFFRACTIONr_scangle_it4.3334.5786
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 146 -
Rwork0.189 2749 -
all-2895 -
obs--100 %
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)
17.0766-5.71222.20186.2676-1.79762.204-0.00880.28340.1337-0.2341-0.0809-0.0602-0.0241-0.00350.08980.1773-0.0125-0.02470.12220.06710.0666-44.591-14.424-40.167
20.7845-0.3051-0.15931.4708-0.0450.8856-0.0235-0.10020.05570.1702-0.0017-0.0601-0.11730.10430.02510.1119-0.0165-0.02530.08890.00020.0267-40.774-24.369-14.521
31.480.1808-0.25332.6893-0.16751.5389-0.01650.02390.14770.00370.0210.3556-0.1889-0.1992-0.00450.11040.0292-0.02740.04860.01130.0931-54.509-10.034-24.314
40.89380.1869-0.13860.5024-0.0180.5206-0.02940.09760.07-0.1056-0.01450.0183-0.0489-0.0090.04390.1113-0.0018-0.02440.08770.02040.0382-47.278-26.131-33.282
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 16
2X-RAY DIFFRACTION2A17 - 142
3X-RAY DIFFRACTION3A143 - 199
4X-RAY DIFFRACTION4A200 - 276

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