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

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Basic information

Entry
Database: PDB / ID: 3rtg
TitleCrystal structure of tm0922, a fusion of a domain of unknown function and ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Thermotoga maritima soaked with Coenzyme A and ATP
Components
  • Putative uncharacterized protein
  • Unknown peptide, probably from expression host
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 / NAD(P)HX 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-related protein N-terminus / YjeF N-terminal domain ...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-related protein N-terminus / YjeF N-terminal domain / YjeF N-terminal domain superfamily / 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 / COENZYME A / : / 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: 2.052 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
DepositionMay 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 19, 2012Group: Database references
Revision 1.3Oct 31, 2012Group: Database references
Revision 1.4Apr 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.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
Revision 1.5Sep 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: Putative uncharacterized protein
B: Unknown peptide, probably from expression host
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2088
Polymers55,3352
Non-polymers2,8736
Water2,936163
1
A: Putative uncharacterized protein
B: Unknown peptide, probably from expression host
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)465,66264
Polymers442,67616
Non-polymers22,98548
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 area75370 Å2
ΔGint-193 kcal/mol
Surface area130590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.245, 122.245, 155.525
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 Putative uncharacterized protein


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: tm0922, TM_0922 / Plasmid: pMH1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9X024, ATP-dependent NAD(P)H-hydrate dehydratase
#2: Protein/peptide Unknown peptide, probably from expression host


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) / Strain: BL21(DE3)

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Non-polymers , 5 types, 169 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-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#6: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 53.14 %
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
Diffraction measurementDetails: 1.00 degrees, 4.6 sec, detector distance 190.00 mm / Method: \w scans
RadiationMonochromator: DIAMOND [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionAv R equivalents: 0.079 / Number: 261313
ReflectionResolution: 2.05→50 Å / Num. all: 37125 / Num. obs: 36107 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 22.524
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.634 / Mean I/σ(I) obs: 2.543 / Rsym value: 0.634 / % possible all: 96.2
Cell measurementReflection used: 261313

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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: 2.052→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / Occupancy max: 1 / Occupancy min: 0.6 / SU B: 6.444 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.196 1811 5 %RANDOM
Rwork0.163 ---
obs0.165 36106 97.27 %-
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: 171.48 Å2 / Biso mean: 31.735 Å2 / Biso min: 13.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20 Å2
2---0.44 Å20 Å2
3---0.89 Å2
Refinement stepCycle: LAST / Resolution: 2.052→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3778 0 154 163 4095
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223998
X-RAY DIFFRACTIONr_bond_other_d00.022658
X-RAY DIFFRACTIONr_angle_refined_deg1.7672.0355439
X-RAY DIFFRACTIONr_angle_other_deg4.1836535
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1215494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44724.539152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.52515684
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8121521
X-RAY DIFFRACTIONr_chiral_restr0.1010.2630
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214290
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02737
X-RAY DIFFRACTIONr_mcbond_it0.9921.52447
X-RAY DIFFRACTIONr_mcbond_other01.51021
X-RAY DIFFRACTIONr_mcangle_it1.81323949
X-RAY DIFFRACTIONr_scbond_it3.07431551
X-RAY DIFFRACTIONr_scangle_it5.1824.51490
LS refinement shellResolution: 2.052→2.105 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 133 -
Rwork0.202 2437 -
all-2570 -
obs--94.17 %
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)
1311.6964193.6753-31.8334137.4088-19.976240.06326.27524.174214.00836.1761-5.63358.2439-1.57712.4997-0.64170.5377-0.32790.05271.3136-0.07961.308551.3311.50718.989
22.9994-2.30130.2142.2735-0.01221.21350.0099-0.12120.12340.0144-0.005-0.05530.063-0.0134-0.00490.0014-0.00530.00110.0836-0.03240.012846.9111.2986.851
32.0374-0.5883-0.16111.65770.55341.5467-0.0050.04820.2111-0.180.0385-0.019-0.33210.1397-0.03360.0739-0.03070.00110.0309-0.00670.028247.22618.3592.1
40.5491-0.2596-0.17940.98240.40621.8677-0.0064-0.02480.08750.0896-0.02690.0443-0.0468-0.01450.03340.0102-0.00490.00790.0584-0.04080.040141.05712.14717.494
53.01122.986-0.84153.0174-0.93970.9884-0.15330.14-0.1861-0.23140.1445-0.17360.21060.07240.00880.08560.0093-0.00470.0609-0.06190.084324.088-15.21927.616
61.05720.0670.19790.8284-0.05211.31110.0359-0.1332-0.05670.15260.0204-0.04180.00210.0077-0.05620.0554-0.0016-0.02180.02680.00320.009318.653-6.7652.035
70.55750.12040.03210.6939-0.20720.54930.0483-0.0113-0.04680.0154-0.0058-0.0708-0.00530.0992-0.04260.0036-0.0025-0.0030.046-0.03820.042429.474-1.13736.932
83.4471-1.502-2.28388.93999.30749.8480.04150.23280.1173-0.1852-0.07830.0465-0.1726-0.1550.03680.0356-0.0170.0180.0526-0.01620.030713.528-5.21226.171
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 2
2X-RAY DIFFRACTION2A3 - 37
3X-RAY DIFFRACTION3A38 - 109
4X-RAY DIFFRACTION4A110 - 205
5X-RAY DIFFRACTION5A206 - 233
6X-RAY DIFFRACTION6A234 - 353
7X-RAY DIFFRACTION7A354 - 475
8X-RAY DIFFRACTION8A476 - 489

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