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

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Basic information

Entry
Database: PDB / ID: 3rtc
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 NAD 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 / 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 / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 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: 2.101 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)57,3297
Polymers55,4322
Non-polymers1,8975
Water2,252125
1
A: Putative uncharacterized protein
B: Unknown peptide, probably from expression host
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)458,63356
Polymers443,45316
Non-polymers15,17940
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_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area64960 Å2
ΔGint-283 kcal/mol
Surface area131940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.399, 122.399, 155.122
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: 904.019 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, 130 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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#6: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine 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 / Water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 53.06 %
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, 12.00 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: 0.054 / Number: 310804
ReflectionResolution: 2.1→50 Å / Num. all: 34592 / Num. obs: 34258 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9 % / Biso Wilson estimate: 38.8 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 42.952
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.745 / Mean I/σ(I) obs: 2.923 / Rsym value: 0.745 / % possible all: 98.6
Cell measurementReflection used: 310804

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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: 2.101→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 1 / SU B: 8.315 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.259 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.209 1722 5 %RANDOM
Rwork0.169 ---
obs0.171 34258 99.05 %-
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: 121.83 Å2 / Biso mean: 45.939 Å2 / Biso min: 25 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.101→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3785 0 96 125 4006
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223947
X-RAY DIFFRACTIONr_bond_other_d00.022643
X-RAY DIFFRACTIONr_angle_refined_deg1.7632.0195361
X-RAY DIFFRACTIONr_angle_other_deg4.20636500
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0445495
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.47524.539152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.17415684
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6251521
X-RAY DIFFRACTIONr_chiral_restr0.1040.2631
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214279
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02736
X-RAY DIFFRACTIONr_mcbond_it0.8911.52453
X-RAY DIFFRACTIONr_mcbond_other01.51022
X-RAY DIFFRACTIONr_mcangle_it1.63123960
X-RAY DIFFRACTIONr_scbond_it2.89131494
X-RAY DIFFRACTIONr_scangle_it4.8494.51401
LS refinement shellResolution: 2.101→2.156 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 137 -
Rwork0.216 2303 -
all-2440 -
obs--96.83 %
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)
127.9669-3.6069-16.826615.7487-10.071618.83830.87771.74010.3079-1.1825-0.51030.55250.3781-0.6929-0.36740.1932-0.138-0.18930.55530.21140.267-54.7551-4.1569-14.9095
21.6097-0.07280.18782.1615-1.3053.4147-0.0554-0.06350.10360.39390.1598-0.0137-0.4167-0.2454-0.10440.08430.05410.01740.16530.04690.0567-46.158312.301-2.7157
39.7052-2.6964-1.65568.38491.8137-0.5129-0.61-0.04731.30870.85850.7539-0.4612-0.6582-0.1516-0.14391.30910.5075-0.05610.3405-0.00760.1982-46.504325.0519-1.4128
41.28260.29470.00311.4464-0.91083.6288-0.01950.0490.1327-0.13940.0516-0.0756-0.0548-0.1322-0.03220.0183-0.00010.01760.12710.05080.0818-41.109911.1167-17.8868
50.823-0.17140.21420.66540.19050.133-0.0031-0.0375-0.1988-0.00030.05590.09590.0098-0.0009-0.05280.0949-0.0006-0.01630.07010.04220.113-17.8643-11.4925-36.4029
62.2098-0.1569-0.12811.45720.01341.7130.05190.3252-0.0943-0.27180.0150.11370.0221-0.0908-0.06680.11670.0002-0.05280.0942-0.00740.0298-19.5795-7.1131-53.8805
71.1351-0.3518-0.04281.34290.37841.10140.07150.0349-0.1151-0.0695-0.03010.1909-0.0178-0.1908-0.04140.0414-0.0058-0.01080.10210.05140.1143-31.783-2.2526-38.3711
81.10530.09960.36774.7733-0.56670.83660.0021-0.12610.01020.182-0.0168-0.03870.0277-0.00030.01470.05870.01180.0130.10810.02320.094-13.4640.4564-26.9697
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 13
2X-RAY DIFFRACTION2A14 - 90
3X-RAY DIFFRACTION3A91 - 109
4X-RAY DIFFRACTION4A110 - 209
5X-RAY DIFFRACTION5A210 - 261
6X-RAY DIFFRACTION6A262 - 352
7X-RAY DIFFRACTION7A353 - 460
8X-RAY DIFFRACTION8A461 - 489

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