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

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Basic information

Entry
Database: PDB / ID: 3rss
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 NADP
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
: / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 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: 1.953 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 2, 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_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
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)56,2144
Polymers55,4322
Non-polymers7832
Water3,315184
1
A: Putative uncharacterized protein
B: Unknown peptide, probably from expression host
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)449,71332
Polymers443,45316
Non-polymers6,26016
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 area50290 Å2
ΔGint-185 kcal/mol
Surface area137190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.271, 122.271, 154.879
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

#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)
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 19-ID / Wavelength: 0.97857 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 14, 2009 / Details: MIRRORS
Diffraction measurementDetails: 1.00 degrees, 1.00 sec, detector distance 280.00 mm
Method: \w scans
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionAv R equivalents: 0.059 / Number: 403298
ReflectionResolution: 1.95→50 Å / Num. all: 42771 / Num. obs: 42559 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.5 % / Biso Wilson estimate: 31.1 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 39.959
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 2.62 / Rsym value: 0.717 / % possible all: 100
Cell measurementReflection used: 403298

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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: 1.953→50 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / Occupancy max: 1 / Occupancy min: 0.6 / SU B: 5.319 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.197 2145 5 %RANDOM
Rwork0.159 ---
obs0.16 42559 99.52 %-
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: 105.18 Å2 / Biso mean: 37.94 Å2 / Biso min: 23.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å20 Å2
2---0.59 Å20 Å2
3---1.17 Å2
Refinement stepCycle: LAST / Resolution: 1.953→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3829 0 41 184 4054
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223937
X-RAY DIFFRACTIONr_bond_other_d00.022651
X-RAY DIFFRACTIONr_angle_refined_deg1.691.9975336
X-RAY DIFFRACTIONr_angle_other_deg4.19136515
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0675500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.54524.423156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.73415688
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8161521
X-RAY DIFFRACTIONr_chiral_restr0.110.2627
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214316
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02743
X-RAY DIFFRACTIONr_mcbond_it1.0591.52477
X-RAY DIFFRACTIONr_mcbond_other01.51032
X-RAY DIFFRACTIONr_mcangle_it1.91923997
X-RAY DIFFRACTIONr_scbond_it3.15331460
X-RAY DIFFRACTIONr_scangle_it5.264.51339
LS refinement shellResolution: 1.953→2.004 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 143 -
Rwork0.189 2957 -
all-3100 -
obs--98.88 %
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)
13.70932.0475-0.37783.9038-0.17382.14210.112-0.23270.10840.4388-0.07980.0735-0.00560.1781-0.03220.1920.01260.04570.0689-0.00990.00640.10348.31810.24
21.48510.0773-0.68070.8934-0.35232.37190.00920.0649-0.0824-0.00170.00020.14330.0212-0.2532-0.00930.1071-0.00770.03970.0413-0.00530.046-14.19943.46710.766
30.8636-0.2650.17210.9693-0.08760.73860.024-0.08020.15140.06820.0372-0.0992-0.09450.0301-0.06130.0816-0.01260.03180.0709-0.02450.04745.1923.28641.764
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 34
2X-RAY DIFFRACTION2A35 - 209
3X-RAY DIFFRACTION3A210 - 489

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