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Basic information

Entry
Database: PDB / ID: 3rrf
TitleCrystal structure of tm0922, a fusion of a domain of unknown function and ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Thermotoga maritima in complex with ATP
Components
  • Bifunctional NAD(P)H-hydrate repair enzyme Nnr
  • peptide
KeywordsLYASE / Unknown function / ADP/ATP-dependent NAD(P)H-hydrate dehydratase
Function / homology
Function and homology information


NAD(P)H-hydrate epimerase / 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 / metal ion binding
Similarity search - Function
Bifunctional NAD(P)H-hydrate repair enzyme Nnr / YjeF N-terminal domain / 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. / YjeF N-terminal domain superfamily / YjeF-related protein N-terminus ...Bifunctional NAD(P)H-hydrate repair enzyme Nnr / YjeF N-terminal domain / 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. / YjeF N-terminal domain superfamily / YjeF-related protein N-terminus / YjeF N-terminal domain / YjeF N-terminal domain profile. / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / Bifunctional NAD(P)H-hydrate repair enzyme Nnr
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsShumilin, I.A. / Cymborowski, M. / Lesley, S.A. / Minor, W.
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 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2 / entity / entity_src_gen / entity_src_nat / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref / struct_ref_seq / 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 / _entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_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.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_ref_seq_dif.details / _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: Bifunctional NAD(P)H-hydrate repair enzyme Nnr
B: peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5047
Polymers55,3352
Non-polymers1,1705
Water2,414134
1
A: Bifunctional NAD(P)H-hydrate repair enzyme Nnr
B: peptide
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)452,03556
Polymers442,67616
Non-polymers9,35940
Water28816
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
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area41040 Å2
ΔGint-131 kcal/mol
Surface area136350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.407, 122.407, 155.672
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Bifunctional NAD(P)H-hydrate repair enzyme Nnr


Mass: 54527.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: nnr / Plasmid: pMH1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9X024
#2: Protein/peptide peptide /


Mass: 806.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Unknown peptide, probably from expression host / Source: (natural) Escherichia coli (E. coli)

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Non-polymers , 5 types, 139 molecules

#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: 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
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.63 Å3/Da / Density % sol: 53.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Na Cacodylate, 1.6 M Na Citrate, pH 6.5, 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: Jun 11, 2009 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 300519 / Num. obs: 300519 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.6 % / Biso Wilson estimate: 33.4 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 28.383
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 8 % / Rmerge(I) obs: 0.882 / Mean I/σ(I) obs: 2.377 / Rsym value: 0.882 / % possible all: 99.8

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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 2AX3

2ax3


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.6 / SU B: 7.472 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.202 1746 5 %RANDOM
Rwork0.159 ---
obs0.161 34755 99.91 %-
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: 110.93 Å2 / Biso mean: 39.205 Å2 / Biso min: 20.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å20 Å20 Å2
2---0.61 Å20 Å2
3---1.22 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3778 0 70 134 3982
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223909
X-RAY DIFFRACTIONr_bond_other_d00.022630
X-RAY DIFFRACTIONr_angle_refined_deg1.7482.015301
X-RAY DIFFRACTIONr_angle_other_deg4.21336461
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9885494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.75824.539152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.14315684
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6121521
X-RAY DIFFRACTIONr_chiral_restr0.1070.2622
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214264
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02742
X-RAY DIFFRACTIONr_mcbond_it0.9061.52447
X-RAY DIFFRACTIONr_mcbond_other01.51021
X-RAY DIFFRACTIONr_mcangle_it1.68823949
X-RAY DIFFRACTIONr_scbond_it2.99431462
X-RAY DIFFRACTIONr_scangle_it5.0074.51352
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 120 -
Rwork0.201 2425 -
all-2545 -
obs--99.84 %
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)
126.27243.706120.289124.4972-7.761123.3706-0.27951.28040.3884-3.29130.11651.67650.72711.04450.1630.7560.153-0.29930.2249-0.09060.12712.94-53.895-16.537
23.46890.55781.02491.20530.18653.63980.0954-0.37340.07470.0385-0.08010.21220.0899-0.3983-0.01530.1836-0.0222-0.0420.09010.00010.0205-11.217-43.586-2.429
36.2196-1.21251.60733.83120.79883.47630.6333-0.4688-0.247-0.0853-0.34120.50820.7062-1.0748-0.29210.3047-0.2046-0.08560.31090.08030.1017-20.023-51.12-2.541
41.5044-0.16770.75861.4093-0.14793.7179-0.00850.08970.0508-0.033-0.01350.1590.136-0.10820.0220.16520.0005-0.04780.04480.01220.05-11.455-41.073-17.322
51.10220.6001-0.4040.79520.3980.22750.0721-0.0444-0.10840.0673-0.0222-0.18270.03380.0635-0.04990.13340.0008-0.03580.1454-0.01790.098611.549-17.747-37.048
61.52410.1814-0.06822.4665-0.01441.550.00580.3021-0.1647-0.3430.0526-0.04670.1356-0.0157-0.05830.1422-0.00590.00730.1648-0.0590.00916.774-20.057-53.989
71.08420.4133-0.26921.19370.08591.0088-0.00230.042-0.21350.00460.0512-0.10580.20430.0058-0.04880.14430.0018-0.060.08910.0010.08861.038-29.378-36.67
814.6276-1.452814.11155.449-3.074117.30890.0623-0.5954-0.03480.3673-0.0252-0.0298-0.0297-0.217-0.03710.123-0.0110.00240.09950.01320.03845.106-13.792-26.176
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 11
2X-RAY DIFFRACTION2A12 - 76
3X-RAY DIFFRACTION3A77 - 108
4X-RAY DIFFRACTION4A109 - 209
5X-RAY DIFFRACTION5A210 - 264
6X-RAY DIFFRACTION6A265 - 352
7X-RAY DIFFRACTION7A353 - 475
8X-RAY DIFFRACTION8A476 - 489

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