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- PDB-3rre: Crystal Structure of tm0922, a fusion of a domain of unknown func... -

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Basic information

Entry
Database: PDB / ID: 3rre
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
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 / 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 / : / 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: 2.15 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_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

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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)56,7728
Polymers55,3352
Non-polymers1,4376
Water2,522140
1
A: Bifunctional NAD(P)H-hydrate repair enzyme Nnr
B: peptide
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)454,17364
Polymers442,67616
Non-polymers11,49748
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 area40240 Å2
ΔGint-135 kcal/mol
Surface area138160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.309, 122.309, 155.312
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: 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)

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Non-polymers , 5 types, 146 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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#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.: 140 / 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: 53.13 %
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: 0.97857 Å
DetectorType: SBC-3 / Detector: CCD / Date: Jul 9, 2008 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 251926 / Num. obs: 251926 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.9 % / Biso Wilson estimate: 33.5 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 20.724
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.839 / Mean I/σ(I) obs: 1.986 / Rsym value: 0.839 / % possible all: 96.2

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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: 2.15→35.42 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.213 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / 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
Rfree0.197 1617 5.1 %RANDOM
Rwork0.161 ---
obs0.163 31868 98.78 %-
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: 101.1 Å2 / Biso mean: 37.85 Å2 / Biso min: 19.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å20 Å2
2---0.47 Å20 Å2
3---0.94 Å2
Refinement stepCycle: LAST / Resolution: 2.15→35.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3778 0 89 140 4007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223940
X-RAY DIFFRACTIONr_bond_other_d00.022644
X-RAY DIFFRACTIONr_angle_refined_deg1.7482.0165348
X-RAY DIFFRACTIONr_angle_other_deg4.2136496
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1795496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69124.575153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.21415685
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0451521
X-RAY DIFFRACTIONr_chiral_restr0.1020.2627
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214299
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02750
X-RAY DIFFRACTIONr_mcbond_it0.8211.52454
X-RAY DIFFRACTIONr_mcbond_other01.51023
X-RAY DIFFRACTIONr_mcangle_it1.55423962
X-RAY DIFFRACTIONr_scbond_it2.8231486
X-RAY DIFFRACTIONr_scangle_it4.684.51386
LS refinement shellResolution: 2.151→2.207 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 113 -
Rwork0.206 2111 -
all-2224 -
obs--96.24 %
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)
123.586-2.705313.02523.6982-21.68130.0698-0.05971.6293-0.1026-1.5904-0.05171.78621.04520.4790.11140.47630.0375-0.18740.2431-0.14830.27052.94-53.895-16.537
22.89950.27690.53371.0209-0.00532.62410.0039-0.26520.1420.0516-0.03170.1342-0.0895-0.24780.02780.195-0.0037-0.02920.09020.0010.0291-11.217-43.586-2.429
35.5375-2.13661.06754.55030.1234.7070.2303-0.2088-0.1554-0.0109-0.14360.72060.4376-0.9422-0.08670.1852-0.1255-0.02740.20560.02710.1216-20.023-51.12-2.541
40.9498-0.35870.55091.4345-0.2083.3276-0.02850.12110.049-0.0621-0.02690.13830.0446-0.16230.05540.1945-0.0033-0.04240.05590.01510.0586-11.455-41.073-17.322
50.94550.3293-0.3270.94680.16470.01570.0939-0.0607-0.0850.0717-0.0304-0.19420.00260.0584-0.06340.16720.0085-0.02920.1685-0.02280.102611.549-17.747-37.048
61.67560.3446-0.0652.73870.04422.09090.00570.2767-0.1382-0.34370.0492-0.09690.10940.006-0.05490.1389-0.00110.00540.1661-0.05460.00636.774-20.057-53.989
71.34750.3169-0.21991.04640.03171.084-0.00440.0349-0.17660.0250.0556-0.11470.20950.0169-0.05120.1671-0.0047-0.05270.1080.00790.07331.038-29.378-36.67
818.7256-2.119416.65016.4347-2.768718.18130.1722-0.6098-0.31230.53620.12550.0961-0.1378-0.1983-0.29770.1553-0.0119-0.00130.12940.02030.05255.106-13.792-26.176
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 11
2X-RAY DIFFRACTION2A12 - 76
3X-RAY DIFFRACTION3A77 - 108
4X-RAY DIFFRACTION4A109 - 209
5X-RAY DIFFRACTION5A210 - 264
6X-RAY DIFFRACTION6A265 - 352
7X-RAY DIFFRACTION7A353 - 475
8X-RAY DIFFRACTION8A476 - 489

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