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- PDB-3r13: Crystal structure of a Deoxyribose-phosphate aldolase (TM_1559) f... -

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Basic information

Entry
Database: PDB / ID: 3r13
TitleCrystal structure of a Deoxyribose-phosphate aldolase (TM_1559) from THERMOTOGA MARITIMA at 1.83 A resolution
ComponentsDeoxyribose-phosphate aldolase
KeywordsLYASE / TIM beta/alpha-barrel / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


deoxyribose phosphate catabolic process / deoxyribose-phosphate aldolase / deoxyribose-phosphate aldolase activity / deoxyribonucleotide catabolic process / carbohydrate catabolic process / cytoplasm
Similarity search - Function
Deoxyribose-phosphate aldolase type I / Deoxyribose-phosphate aldolase / DeoC/LacD family aldolase / DeoC/FbaB/LacD aldolase / DeoC/LacD family aldolase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Unknown ligand / Deoxyribose-phosphate aldolase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.83 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Deoxyribose-phosphate aldolase (TM_1559) from THERMOTOGA MARITIMA at 1.83 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _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: Deoxyribose-phosphate aldolase
B: Deoxyribose-phosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,85712
Polymers58,3182
Non-polymers53810
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-27 kcal/mol
Surface area20980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.904, 52.481, 85.462
Angle α, β, γ (deg.)90.00, 95.59, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A1 - 205
2115B1 - 205

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Components

#1: Protein Deoxyribose-phosphate aldolase / / Phosphodeoxyriboaldolase / DERA / Deoxyriboaldolase


Mass: 29159.082 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: deoC, TM1559, TM_1559 / Plasmid: MH1 / Production host: Escherichia Coli (E. coli) / Strain (production host): DL41 / References: UniProt: Q9X1P5, deoxyribose-phosphate aldolase
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH.

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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: 2.06 Å3/Da / Density % sol: 40.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 40.0% 1,2-propanediol, 0.05M calcium acetate, 0.1M acetate pH 4.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.89194,0.97946,0.97929
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 31, 2005 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.891941
20.979461
30.979291
ReflectionResolution: 1.83→44.677 Å / Num. obs: 42195 / % possible obs: 100 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 8.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.83-1.933.70.5522.42304061740.552100
1.93-2.053.80.43.32147857250.4100
2.05-2.193.80.274.72057154820.27100
2.19-2.363.80.261902450590.2100
2.36-2.593.80.1517.41760946720.151100
2.59-2.893.80.1089.71601942520.108100
2.89-3.343.80.07512.41409337540.075100
3.34-4.093.70.0516.91189931860.05100
4.09-5.793.70.03920.2920924860.039100
5.79-44.6773.60.03421.6500314050.03499.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.2.5data scaling
REFMAC5.5.0110refinement
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.83→44.677 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 6.131 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.12
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. THE ELECTRON DENSITY REVEALS THAT LYSINE 179 HAS BEEN COVALENTLY MODIFIED. IT WAS MODELED AS AN UNKNOWN LIGAND (UNL). 4. ACETATE (ACT) AND GLYCEROL (GOL) MODELED IN THE STRUCTURE ARE PRESENT IN CRYO/PROTEIN BUFFERS. 5. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 6. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.1928 2116 5 %RANDOM
Rwork0.1545 ---
obs0.1564 42154 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.5 Å2 / Biso mean: 25.1014 Å2 / Biso min: 7.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å2-0.01 Å2
2---0.38 Å20 Å2
3---1.17 Å2
Refinement stepCycle: LAST / Resolution: 1.83→44.677 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3978 0 48 259 4285
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224312
X-RAY DIFFRACTIONr_bond_other_d0.0010.022924
X-RAY DIFFRACTIONr_angle_refined_deg1.4321.9545830
X-RAY DIFFRACTIONr_angle_other_deg0.89937160
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9585560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.89723.859184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.51215768
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8441525
X-RAY DIFFRACTIONr_chiral_restr0.0910.2644
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024892
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02877
X-RAY DIFFRACTIONr_mcbond_it1.70832689
X-RAY DIFFRACTIONr_mcbond_other0.59331111
X-RAY DIFFRACTIONr_mcangle_it2.82254343
X-RAY DIFFRACTIONr_scbond_it5.23981623
X-RAY DIFFRACTIONr_scangle_it8.161111483
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1163MEDIUM POSITIONAL0.080.5
1427LOOSE POSITIONAL0.385
1163MEDIUM THERMAL0.752
1427LOOSE THERMAL0.9110
LS refinement shellResolution: 1.83→1.878 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 164 -
Rwork0.259 2932 -
all-3096 -
obs--100 %
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)
11.10870.02960.14350.69840.09250.44050.0110.0768-0.0031-0.0077-0.0157-0.00550.0776-0.01140.00470.039-0.00370.00520.042-0.00620.00463.58923.19754.546
20.79910.07360.1150.49310.12990.59570.0089-0.05280.01720.0881-0.0194-0.01140.0029-0.01570.01050.0363-0.0003-0.00270.0055-0.00380.04857.03143.34477.915
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-9 - 247
2X-RAY DIFFRACTION2B-9 - 248

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