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

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Basic information

Entry
Database: PDB / ID: 3rpz
TitleCrystal Structure of ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Bacillus subtilis co-crystallized with ATP/Mg2+ and soaked with NADPH
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
ADENOSINE MONOPHOSPHATE / Chem-NPW / ADP-dependent (S)-NAD(P)H-hydrate dehydratase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 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 / pdbx_struct_special_symmetry / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_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

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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)31,3114
Polymers30,1761
Non-polymers1,1353
Water4,540252
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)125,24616
Polymers120,7064
Non-polymers4,54012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area15710 Å2
ΔGint-96 kcal/mol
Surface area36510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.920, 91.920, 169.630
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-363-

HOH

21A-370-

HOH

31A-456-

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-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-NPW / BETA-6-HYDROXY-1,4,5,6-TETRAHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE


Mass: 763.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H32N7O18P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.97 Å3/Da / Density % sol: 58.56 %
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, 9.00 sec, detector distance 140.00 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: 0.086 / Number: 281605
ReflectionResolution: 1.51→50 Å / Num. obs: 57168 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 25.913
Cell measurementReflection used: 281605

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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: 1.51→50 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.975 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 1.246 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, refinement counts Friedel's pair. U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.148 2895 5.1 %RANDOM
Rwork0.134 ---
obs0.135 57159 99.96 %-
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: 57.39 Å2 / Biso mean: 21.147 Å2 / Biso min: 11.13 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2---0.38 Å20 Å2
3---0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.51→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2107 0 73 252 2432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222285
X-RAY DIFFRACTIONr_bond_other_d00.021497
X-RAY DIFFRACTIONr_angle_refined_deg2.1552.0063142
X-RAY DIFFRACTIONr_angle_other_deg4.2433681
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2955290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.29424.40993
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.89715356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.151512
X-RAY DIFFRACTIONr_chiral_restr0.1110.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212526
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02429
X-RAY DIFFRACTIONr_mcbond_it1.0431.51398
X-RAY DIFFRACTIONr_mcbond_other01.5568
X-RAY DIFFRACTIONr_mcangle_it1.8922250
X-RAY DIFFRACTIONr_scbond_it2.9483887
X-RAY DIFFRACTIONr_scangle_it4.7134.5885
LS refinement shellResolution: 1.51→1.549 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.157 221 -
Rwork0.144 3943 -
all-4164 -
obs--99.86 %
Refinement TLS params.Method: refined / Origin x: -0.308 Å / Origin y: -24.649 Å / Origin z: -23.727 Å
111213212223313233
T0.0505 Å2-0.0029 Å20.0281 Å2-0.0185 Å2-0.0095 Å2--0.0339 Å2
L0.4311 °2-0.0771 °20.0549 °2-0.643 °20.0316 °2--0.3643 °2
S-0.0286 Å °0.0157 Å °-0.0967 Å °-0.0005 Å °-0.0206 Å °0.017 Å °0.0713 Å °-0.011 Å °0.0492 Å °

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