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- PDB-3rt7: Crystal structure of tm0922, a fusion of a domain of unknown func... -

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Basic information

Entry
Database: PDB / ID: 3rt7
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 ADP-glucose
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'-DIPHOSPHATE-GLUCOSE / : / 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
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: Advisory / Database references ...Advisory / Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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)57,2588
Polymers55,3352
Non-polymers1,9246
Water1,964109
1
A: Putative uncharacterized protein
B: Unknown peptide, probably from expression host
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)458,06464
Polymers442,67616
Non-polymers15,38848
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_554-x,y,-z-11
crystal symmetry operation6_554x,-y,-z-11
crystal symmetry operation7_554y,x,-z-11
crystal symmetry operation8_554-y,-x,-z-11
Buried area64330 Å2
ΔGint-381 kcal/mol
Surface area131290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.138, 122.138, 155.337
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, 115 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-ADQ / ADENOSINE-5'-DIPHOSPHATE-GLUCOSE / ADENOSINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 589.342 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H25N5O15P2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.62 Å3/Da / Density % sol: 53.01 %
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
Diffraction measurementDetails: 1.00 degrees, 8.00 sec, detector distance 180.00 mm
Method: \w 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: 0.057 / Number: 296094
ReflectionResolution: 2.1→50 Å / Num. all: 34667 / Num. obs: 34568 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.6 % / Biso Wilson estimate: 40.4 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 37.91
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.904 / Mean I/σ(I) obs: 2.282 / Rsym value: 0.904 / % possible all: 100
Cell measurementReflection used: 296094

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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: 0.967 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 1 / SU B: 8.693 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.181 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1738 5 %RANDOM
Rwork0.174 ---
obs0.176 34461 99.73 %-
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: 108.63 Å2 / Biso mean: 46.29 Å2 / Biso min: 27.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3778 0 89 109 3976
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223930
X-RAY DIFFRACTIONr_bond_other_d00.022640
X-RAY DIFFRACTIONr_angle_refined_deg1.7262.0165332
X-RAY DIFFRACTIONr_angle_other_deg4.1936485
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1695494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.72524.539152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.8415684
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6131521
X-RAY DIFFRACTIONr_chiral_restr0.1010.2626
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214277
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02748
X-RAY DIFFRACTIONr_mcbond_it0.8791.52447
X-RAY DIFFRACTIONr_mcbond_other01.51021
X-RAY DIFFRACTIONr_mcangle_it1.60123949
X-RAY DIFFRACTIONr_scbond_it2.76831483
X-RAY DIFFRACTIONr_scangle_it4.5684.51383
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 126 -
Rwork0.212 2378 -
all-2504 -
obs--99.92 %
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)
116.03022.64516.543410.183-4.791411.1660.0825-1.2504-0.61130.8473-0.18390.2896-0.5851-0.6310.10140.12380.10030.0660.39120.09410.1034-54.5694.131-63.196
22.0001-0.0868-0.18871.9253-1.15962.7789-0.09260.0327-0.1196-0.32040.15280.00310.3614-0.2157-0.06030.0635-0.0518-0.01090.16670.04290.0266-45.971-12.464-74.967
32.94342.6724-0.004911.65752.2788-0.9939-0.34750.4402-1.126-1.01930.5621-0.1951.3702-0.0476-0.21461.0495-0.2641-0.00580.3287-0.02520.3622-46.401-24.902-76.222
40.9486-0.23980.10071.286-0.88093.2621-0.0447-0.037-0.16120.10.0208-0.03430.0501-0.15690.02390.0070.0034-0.00810.13420.05620.0732-41.065-11.062-59.736
50.8020.2445-0.25980.71120.18580.07940.00780.03040.20630.0230.0640.103-0.01970.0051-0.07180.08820.00020.02090.06420.04960.0979-17.82111.525-41.251
62.22830.13570.0841.56160.04571.80740.0608-0.32110.11420.27790.03290.12850.0074-0.0898-0.09370.1132-0.00020.05630.0856-0.00710.021-19.5437.151-23.781
70.98330.2073-0.07231.03690.26540.78750.07870.0060.08990.0534-0.01610.15450.0054-0.1525-0.06270.03050.00250.00770.09320.0580.0896-29.4791.176-40.589
83.8612-1.31940.31459.3451-8.08569.11310.02710.3157-0.0866-0.34450.0457-0.0940.08380.0634-0.07290.0775-0.0173-0.00860.11260.01270.0869-13.5115.219-51.474
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 14
2X-RAY DIFFRACTION2A15 - 90
3X-RAY DIFFRACTION3A91 - 109
4X-RAY DIFFRACTION4A110 - 209
5X-RAY DIFFRACTION5A210 - 261
6X-RAY DIFFRACTION6A262 - 352
7X-RAY DIFFRACTION7A353 - 475
8X-RAY DIFFRACTION8A476 - 489

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