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- PDB-2ax3: CRYSTAL STRUCTURE OF A PUTATIVE CARBOHYDRATE KINASE (TM0922) FROM... -

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Basic information

Entry
Database: PDB / ID: 2ax3
TitleCRYSTAL STRUCTURE OF A PUTATIVE CARBOHYDRATE KINASE (TM0922) FROM THERMOTOGA MARITIMA MSB8 AT 2.25 A RESOLUTION
Components
  • hypothetical protein TM0922
  • unknown peptide
KeywordsTRANSFERASE / PUTATIVE CARBOHYDRATE KINASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
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
Bifunctional NAD(P)H-hydrate repair enzyme Nnr
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.27 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (tm0922) from THERMOTOGA MARITIMA at 2.27 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein TM0922
B: unknown peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9103
Polymers55,8182
Non-polymers921
Water3,099172
1
A: hypothetical protein TM0922
B: unknown peptide
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)447,28024
Polymers446,54316
Non-polymers7378
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 area43790 Å2
ΔGint-144 kcal/mol
Surface area126350 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)121.264, 121.264, 153.873
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 hypothetical protein TM0922


Mass: 54902.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: tm0922 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X024
#2: Protein/peptide unknown peptide


Mass: 915.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Unknown peptide, probably from expression host
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 52.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6.5
Details: 1.6M NaCl, 0.1M Cacodylate, pH 6.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979245, 0.979078, 0.891940
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 28, 2005 / Details: double crystal monochromator
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9792451
20.9790781
30.891941
ReflectionResolution: 2.26→28.89 Å / Num. obs: 27157 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.111 / Rsym value: 0.111 / Net I/σ(I): 6.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsRsym value
2.26-2.381006.40.661.239020.66
2.38-2.531007.30.5611.336980.561
2.53-2.71007.10.4341.734800.434
2.7-2.921007.30.2862.632570.286
2.92-3.21007.20.1664.530150.166
3.2-3.5710070.0927.827300.092
3.57-4.1399.96.80.06510.424190.065
4.13-5.0510070.05212.520790.052
5.05-7.151006.60.0541216420.054
7.15-28.8998.56.10.03716.49350.037

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT1.601data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.27→28.89 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.923 / SU B: 11.459 / SU ML: 0.14 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.233 / ESU R Free: 0.198
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. A SMALL PEPTIDE IS BOUND WHICH CO-PURIFIED WITH TM0922. THE PEPTIDE IS LIKELY FROM THE E. COLI EXPRESSION HOST AND IS OF UNKNOWN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. A SMALL PEPTIDE IS BOUND WHICH CO-PURIFIED WITH TM0922. THE PEPTIDE IS LIKELY FROM THE E. COLI EXPRESSION HOST AND IS OF UNKNOWN SEQUENCE. IT HAS BEEN MODELED AS A 8 RESIDUE PEPTIDE. RESIDUES 3-6 HAVE THE BEST DENSITY. BASED ON DENSITY RESIDUES 3,5 AND 6 WERE ASSIGNED AS TRP, PHE AND HIS. RESIDUE 4 IS LIKELY A CYS OR SER, BUT HAS BEEN MODELED AS UNK ALONG WITH THE REMAINING RESIDUES.
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1349 5.1 %RANDOM
Rwork0.159 ---
all0.162 ---
obs-25250 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20 Å2
2---0.27 Å20 Å2
3---0.54 Å2
Refinement stepCycle: LAST / Resolution: 2.27→28.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3682 0 6 172 3860
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223790
X-RAY DIFFRACTIONr_bond_other_d0.0030.023591
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.9795156
X-RAY DIFFRACTIONr_angle_other_deg0.80638294
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3745509
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9424.388139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.5915620
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5461517
X-RAY DIFFRACTIONr_chiral_restr0.0860.2618
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024265
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02731
X-RAY DIFFRACTIONr_nbd_refined0.2080.2836
X-RAY DIFFRACTIONr_nbd_other0.1740.23815
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21935
X-RAY DIFFRACTIONr_nbtor_other0.0880.22470
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2175
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2560.2109
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.215
X-RAY DIFFRACTIONr_mcbond_it2.18332551
X-RAY DIFFRACTIONr_mcbond_other0.52431042
X-RAY DIFFRACTIONr_mcangle_it3.1253996
X-RAY DIFFRACTIONr_scbond_it5.9781383
X-RAY DIFFRACTIONr_scangle_it7.842111156
LS refinement shellResolution: 2.27→2.331 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 101 -
Rwork0.195 1698 -
obs--92.78 %
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)
10.71930.153-0.2711.37350.90323.3776-0.0568-0.01350.1411-0.07350.09740.0274-0.22550.2062-0.0406-0.1262-0.0066-0.00430.016-0.0324-0.03943.577211.623510.3546
20.8960.5213-0.06660.9593-0.24351.06220.035-0.0695-0.15490.08620.0266-0.17880.02450.1485-0.0616-0.1110.0204-0.0217-0.0949-0.0295-0.066122.974-5.045141.3345
30.48653.48083.690528.274521.191736.0702-0.0611-0.39490.60740.8207-0.19830.97560.6531-1.80060.25940.139-0.03280.05340.3415-0.01710.239534.0929-3.05278.4528
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-1 - 20911 - 221
2X-RAY DIFFRACTION2AA210 - 489222 - 501
3X-RAY DIFFRACTION3BB1 - 81 - 8

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