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- PDB-3rrj: Crystal structure of tm0922, a fusion of a domain of unknown func... -

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Entry
Database: PDB / ID: 3rrj
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 P1,P5-Di(adenosine-5') pentaphosphate
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
BIS(ADENOSINE)-5'-PENTAPHOSPHATE / : / 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: 2.5 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_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

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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)56,3115
Polymers55,2632
Non-polymers1,0483
Water88349
1
A: Bifunctional NAD(P)H-hydrate repair enzyme Nnr
B: peptide
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)450,48840
Polymers442,10816
Non-polymers8,38024
Water1448
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_556-x,y,-z+11
crystal symmetry operation6_556x,-y,-z+11
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_556-y,-x,-z+11
Buried area40370 Å2
ΔGint-156 kcal/mol
Surface area138260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.947, 121.947, 155.257
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: 735.826 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 , 4 types, 52 molecules

#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-AP5 / BIS(ADENOSINE)-5'-PENTAPHOSPHATE


Mass: 916.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H29N10O22P5
#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.61 Å3/Da / Density % sol: 52.89 %
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: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 16, 2009 / Details: BERYLLIUM LENSES
RadiationMonochromator: DIAMOND [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 174277 / Num. obs: 174277 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.6 % / Biso Wilson estimate: 51.2 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 26.659
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.649 / Mean I/σ(I) obs: 2.312 / Rsym value: 0.649 / % possible all: 95.6

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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: 2.5→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 1 / SU B: 16.88 / SU ML: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1031 5.1 %RANDOM
Rwork0.166 ---
obs0.169 20035 97.23 %-
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: 79.12 Å2 / Biso mean: 45.442 Å2 / Biso min: 10.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å20 Å2
2---0.39 Å20 Å2
3---0.78 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3773 0 38 49 3860
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223871
X-RAY DIFFRACTIONr_bond_other_d0.0010.022616
X-RAY DIFFRACTIONr_angle_refined_deg1.64125242
X-RAY DIFFRACTIONr_angle_other_deg0.94136429
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2215493
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.73724.539152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.98915684
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2811521
X-RAY DIFFRACTIONr_chiral_restr0.0890.2617
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214241
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02729
X-RAY DIFFRACTIONr_mcbond_it0.6931.52442
X-RAY DIFFRACTIONr_mcbond_other0.1471.51019
X-RAY DIFFRACTIONr_mcangle_it1.36323942
X-RAY DIFFRACTIONr_scbond_it2.33931429
X-RAY DIFFRACTIONr_scangle_it3.8264.51300
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 62 -
Rwork0.245 1370 -
all-1432 -
obs--96.11 %
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)
199.4432-41.1974-1.817744.09127.375453.3769-0.77011.7044-4.8968-0.9972-0.57981.9218-0.57683.12951.34990.0732-0.03470.0790.6499-0.14040.276451.3910.91459.205
20.65320.19750.42853.58860.8853.1667-0.08990.0597-0.14020.2550.197-0.08620.29920.4412-0.10710.04220.05620.00010.3016-0.05510.044947.245-10.64574.236
38.0945-1.48671.88982.4395.844910.72720.15490.0187-1.75471.02730.18880.24081.76420.5669-0.34370.46140.0734-0.04540.10030.05590.347244.084-26.20175.292
41.16260.70360.84492.42890.85833.9977-0.04450.1486-0.1273-0.17250.02220.06480.0560.29110.0223-0.00110.01510.00430.2453-0.07550.097541.02-11.10659.546
55.2541-5.47040.45828.1547-1.91390.8317-0.2476-0.36650.32820.5730.4067-0.0371-0.2815-0.0501-0.15910.1603-0.04220.03550.1478-0.12880.139320.58317.16849.647
62.6447-0.106-0.10861.48430.52642.61870.04880.30720.1566-0.22440.0459-0.05350.02370.0289-0.09470.147800.04870.1151-0.00390.028218.5996.73325.467
70.9446-0.42070.21442.0969-0.55531.20720.11110.03750.1238-0.1096-0.0818-0.18070.03690.2333-0.02920.0594-0.00360.02260.1855-0.08470.109431.7262.25139.289
80.7435-0.87060.57378.46741.7441.2143-0.007-0.1016-0.04520.35810.01460.23740.0576-0.0074-0.00760.1191-0.01520.02890.1695-0.04070.08213.409-0.48550.61
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 5
2X-RAY DIFFRACTION2A6 - 92
3X-RAY DIFFRACTION3A93 - 110
4X-RAY DIFFRACTION4A111 - 209
5X-RAY DIFFRACTION5A210 - 233
6X-RAY DIFFRACTION6A234 - 352
7X-RAY DIFFRACTION7A353 - 461
8X-RAY DIFFRACTION8A462 - 489

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