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- PDB-6d33: Crystal structure of BH1352 2-deoxyribose-5-phosphate from Bacill... -

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Basic information

Entry
Database: PDB / ID: 6d33
TitleCrystal structure of BH1352 2-deoxyribose-5-phosphate from Bacillus halodurans
ComponentsDeoxyribose-phosphate aldolase
KeywordsTRANSFERASE / aldolase / TIM barrel / 2-deoxyribose-5-phosphate / DRP
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
Deoxyribose-phosphate aldolase
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.502 Å
AuthorsStogios, P.J. / Skarina, T. / Kim, T. / Yim, V. / Yakunin, A. / Savchenko, A.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)Industrial Biocatalysis Network Canada
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Rational engineering of 2-deoxyribose-5-phosphate aldolases for the biosynthesis of (R)-1,3-butanediol.
Authors: Kim, T. / Stogios, P.J. / Khusnutdinova, A.N. / Nemr, K. / Skarina, T. / Flick, R. / Joo, J.C. / Mahadevan, R. / Savchenko, A. / Yakunin, A.F.
History
DepositionApr 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: Deoxyribose-phosphate aldolase
D: Deoxyribose-phosphate aldolase
E: Deoxyribose-phosphate aldolase
F: Deoxyribose-phosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,09824
Polymers140,3206
Non-polymers1,77818
Water8,017445
1
A: Deoxyribose-phosphate aldolase
B: Deoxyribose-phosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,54010
Polymers46,7732
Non-polymers7678
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-15 kcal/mol
Surface area17940 Å2
MethodPISA
2
C: Deoxyribose-phosphate aldolase
D: Deoxyribose-phosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2947
Polymers46,7732
Non-polymers5215
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-17 kcal/mol
Surface area16770 Å2
MethodPISA
3
E: Deoxyribose-phosphate aldolase
F: Deoxyribose-phosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2647
Polymers46,7732
Non-polymers4915
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-20 kcal/mol
Surface area17390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)240.908, 55.523, 177.706
Angle α, β, γ (deg.)90.00, 128.02, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Deoxyribose-phosphate aldolase / / DERA / 2-deoxy-D-ribose 5-phosphate aldolase / Phosphodeoxyriboaldolase / Deoxyriboaldolase


Mass: 23386.732 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125) (bacteria)
Strain: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125
Gene: deoC, dra, BH1352 / Plasmid: p15Tv lic / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Gold / References: UniProt: Q9KD67, deoxyribose-phosphate aldolase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 3.34 Å3/Da / Density % sol: 63.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris pH 8.5, 0.2 M MgCl2, 25% (w/v) PEG 3350, 10 mM acetaldehyde

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 63816 / % possible obs: 98.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.027 / Net I/σ(I): 34.23
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 2.56 / Num. unique obs: 3103 / CC1/2: 0.75 / Rpim(I) all: 0.392 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIXdev_3092refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NGJ

3ngj


Resolution: 2.502→30.021 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2505 1995 3.13 %RANDOM
Rwork0.2051 ---
obs0.2065 63680 98.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.502→30.021 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9515 0 116 445 10076
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049752
X-RAY DIFFRACTIONf_angle_d0.63513181
X-RAY DIFFRACTIONf_dihedral_angle_d21.1653580
X-RAY DIFFRACTIONf_chiral_restr0.0431613
X-RAY DIFFRACTIONf_plane_restr0.0041683
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5018-2.56440.3351330.29864180X-RAY DIFFRACTION94
2.5644-2.63360.3411390.28484371X-RAY DIFFRACTION98
2.6336-2.71110.33991500.28494293X-RAY DIFFRACTION98
2.7111-2.79850.30811390.2764372X-RAY DIFFRACTION98
2.7985-2.89850.33831380.26154348X-RAY DIFFRACTION98
2.8985-3.01440.2961440.25454357X-RAY DIFFRACTION98
3.0144-3.15150.33141340.26424391X-RAY DIFFRACTION99
3.1515-3.31740.29051450.25464383X-RAY DIFFRACTION98
3.3174-3.5250.30281410.22744401X-RAY DIFFRACTION98
3.525-3.79670.26911470.20194423X-RAY DIFFRACTION99
3.7967-4.17780.20391370.18374481X-RAY DIFFRACTION100
4.1778-4.78030.20671510.15464494X-RAY DIFFRACTION100
4.7803-6.01470.26771430.18484534X-RAY DIFFRACTION100
6.0147-30.0230.18051540.17354657X-RAY DIFFRACTION100
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)
13.75561.46720.94885.1072-4.09214.7078-0.0152-0.0810.05010.4592-0.29090.404-0.6868-1.04140.39970.39790.0371-0.08850.5977-0.18030.6521-55.0098-9.04680.9652
28.1273-1.199-5.38018.7132.94559.1857-0.32660.89640.2102-0.1485-0.21240.8503-0.7666-0.9160.51640.47870.0421-0.19780.441-0.09040.5967-53.3403-5.0254-7.6535
37.0881-4.0310.61337.1234-0.08555.1242-0.47570.26990.23050.2125-0.02860.0144-0.38530.1970.46310.3574-0.0654-0.06950.27740.00950.3273-38.0021-11.1871-2.058
46.5855-0.84860.42047.7285-0.61147.7141-0.3185-0.2255-0.25040.6667-0.0995-0.17680.31520.95340.40650.42910.0211-0.01790.35780.03760.3443-34.312-15.63587.7847
53.6059-1.482-0.40982.0012-0.26044.2968-0.423-0.0454-0.23840.2574-0.17430.35970.313-0.39760.58060.4796-0.05960.07730.3129-0.07350.5635-49.0543-15.789610.612
64.5718-3.766-6.36836.59183.50729.73910.0892-0.08690.41040.48071.01730.5927-0.451-0.5966-1.16940.68790.04740.0140.758-0.08640.8515-69.099-8.07927.5556
76.8532-2.3630.05627.76755.29966.3761-0.33580.0222-1.03680.79120.23060.05021.22650.27190.08670.79530.11240.25460.53750.07320.6976-29.3826-37.201-9.4186
83.6789-1.7271-1.77389.37857.04246.5111-0.56730.1259-0.32150.63730.4908-0.17560.96550.73780.10750.65110.06680.08840.57120.120.5348-25.6705-30.4198-9.7816
98.4993-2.19420.55154.97111.06045.18740.11480.8036-0.4765-0.3498-0.3094-0.28570.3611.29060.17430.45080.01850.12120.66320.00670.492-29.0587-26.29-14.1532
109.2658-1.20050.46062.73991.44755.4832-0.21460.43870.0921-0.3747-0.0872-0.0511-0.33840.22380.32120.5184-0.12270.05680.45190.04920.3614-36.3626-17.6664-20.0418
114.57126.3235-3.93789.85-2.96469.4262-1.54940.91710.7638-1.66530.58740.73560.446-0.56390.86420.7579-0.0675-0.08510.7057-0.07580.497-45.1401-21.1423-29.5821
125.73891.4913-1.53834.6357-2.86574.4276-0.32990.537-0.5381-0.0718-0.02590.3451.0328-0.03150.33260.7201-0.14260.1980.5589-0.1370.6168-41.6391-33.5186-24.1443
138.7778-1.72064.98186.3354-4.54164.94240.328-0.3441-0.9734-0.2056-0.1502-0.14381.1794-0.0607-0.0891.0160.09760.2880.5689-0.1450.9094-34.7025-42.9715-18.7151
145.8097-1.23662.98629.02681.15497.7641-0.7451-0.98271.0344-0.3415-0.45371.1757-0.3291-1.12741.35110.69730.2036-0.24810.7117-0.19930.9354-47.490410.150228.5731
155.8114-3.0244.12689.4892-2.46366.7026-0.5177-0.74460.36170.40820.28491.4164-0.5377-1.29640.23070.60250.0941-0.09520.9097-0.09160.9406-50.0295.057234.3974
162.74261.1818-0.5074.4504-0.79787.9712-0.44520.05540.4289-0.0770.31720.27620.0615-0.15030.11820.4660.0063-0.19140.4253-0.05070.4903-33.8532.743628.15
175.63375.5064-2.83755.4256-1.70718.5067-0.60560.8615-0.648-0.43510.6477-0.86390.06481.3683-0.06530.5490.0153-0.12870.6893-0.06660.6001-24.8383-0.065121.4302
187.52587.9228-3.11589.8532-3.84196.6557-0.3647-0.28690.29530.29010.06020.1862-0.75570.31020.24850.70970.0108-0.28020.35020.0720.5882-33.56076.522820.6943
199.1317-3.73612.1661.9349-1.68587.6409-0.04610.94530.5981-0.99650.00550.2051-1.05411.2630.00660.8605-0.2829-0.26330.69850.14640.5832-27.69989.119911.8746
203.5266-0.49830.05115.53950.28674.7181-0.21550.05881.0257-0.4946-0.21490.619-1.13-0.50610.34270.95560.0571-0.42260.42230.02140.976-40.693412.248315.2921
219.1845-5.9868-2.52554.231.58620.7022-0.6088-0.84641.1965-0.21910.47050.966-1.5244-0.89610.11680.92540.2996-0.24950.7866-0.20461.2307-50.768312.035821.6076
224.0834-0.7463-1.96857.9153-1.4937.59710.5379-0.8280.82221.3728-0.1691-0.75240.19850.7541-0.27390.8881-0.2136-0.16620.8005-0.13010.8722-14.953623.077639.5387
234.85054.92736.93994.96587.02069.9321-0.126-0.13680.8265-1.22830.509-0.5615-1.26991.8245-0.36331.2738-0.52-0.18791.1529-0.08710.8639-9.263920.600932.1362
244.44395.04721.65566.19271.79452.5755-0.5757-0.83120.64870.10490.3805-0.4841-0.61441.48760.21960.6463-0.182-0.22490.9903-0.16480.683-12.045512.659437.4721
255.2610.90690.60324.88813.74019.2738-0.2615-0.01930.28680.32610.04470.25520.2661-0.05550.14860.49320.0655-0.14930.5428-0.02460.4485-28.67446.713242.315
265.611.31070.68023.02991.62897.45990.0089-0.83810.2232-0.0114-0.25750.415-0.1001-0.67090.21930.58770.1156-0.13930.611-0.14250.4664-29.29958.172649.0716
274.02251.6044-0.91525.4561-0.17266.5911-0.1078-0.24270.77760.3232-0.03510.2532-1.25230.09250.13680.87840.0921-0.23580.6501-0.19610.6648-25.009522.380650.3262
282.62490.54631.14136.32153.08711.79470.3004-0.732-0.52540.270.5371-0.24071.60211.1812-0.93730.93870.22080.11090.92510.01370.6619-20.1376-39.1932-46.8682
295.9211-5.13982.94957.5779-1.91649.8726-0.0269-0.0612-0.677-0.3269-0.2351-0.00931.2098-0.0650.24620.8521-0.05690.19820.5908-0.07360.5952-26.3673-42.0758-51.4279
303.19710.2699-0.92822.4214-4.60339.5586-0.5252-0.2463-0.6488-0.28840.101-0.5021.0162-0.36130.23480.6735-0.04550.16050.7819-0.06590.5325-28.0323-31.9926-48.5612
312.7690.1394-0.44493.6199-0.71835.71940.0005-0.1437-0.010.2774-0.15250.027-0.22650.35310.16630.4951-0.0530.07980.7403-0.10190.392-23.8156-19.8162-44.4975
326.5461-2.23754.53518.7591-1.70563.55180.0277-0.0458-0.35090.15640.0168-0.5361.21211.1698-0.06780.81740.12370.05131.03620.03240.4598-13.3624-29.5167-35.4775
337.70356.49280.2236.3198-1.41763.9983-0.18620.2424-1.01750.1404-0.4417-1.16192.37141.20730.54111.32230.29170.28771.11430.19280.7066-15.4364-41.6586-40.3774
344.98452.0827-3.01519.181-4.28968.90870.21520.23040.44930.1756-0.1784-0.5212-0.60830.2853-0.02280.62-0.18480.00550.8924-0.03780.4867-13.4791-6.8347-65.3759
355.4772.1487-2.84477.952-5.50764.21560.05180.08580.339-0.30540.1439-0.1146-0.5347-0.0027-0.1970.592-0.0632-0.00390.6883-0.1170.3971-21.032-6.9132-63.4701
363.31071.0576-1.09474.71641.80142.4880.4413-0.11930.2794-0.7552-0.63330.3939-0.75850.11250.12030.69340.03850.00640.6687-0.11050.4878-23.807-12.5441-66.2626
373.0097-1.644-0.26076.7426-0.83113.3854-0.3114-0.146-0.10580.43520.09960.54210.1484-0.43280.21740.52530.0533-0.04250.6866-0.10720.4352-28.9761-23.0906-65.3234
385.0274-5.182.35.3754-2.51991.37360.34640.0128-1.1288-1.0478-0.01411.35560.6301-0.9064-0.27330.671-0.1485-0.06330.8681-0.11680.5539-33.4839-27.5478-70.3304
393.9973-4.7598-3.01227.99782.12995.7481-0.1557-0.1847-0.4384-0.4337-0.04970.66460.1416-0.27010.14160.4848-0.0431-0.05580.7096-0.12810.4694-23.5433-23.6214-71.8147
408.8783-5.884-3.09089.72971.08258.7452-0.02231.6913-1.4468-1.0044-0.40720.4530.37380.30130.31680.62990.020.06090.6176-0.20050.4661-23.8453-32.7304-77.7893
414.67070.0209-4.83016.79493.00476.30230.11680.1061-0.145-0.04980.2817-0.360.32511.4268-0.4710.4801-0.0032-0.0540.8097-0.06890.3616-17.1842-23.1521-70.7051
426.96972.2322-0.66435.86630.68250.2190.25990.20360.1894-0.1827-0.1885-0.1807-0.35870.8707-0.11350.6541-0.01110.00630.9058-0.0260.3899-12.7644-20.4614-79.03
438.7389-4.7626-4.08488.59026.66245.26661.0444-0.03231.6746-0.41060.0184-0.8774-0.3937-0.3553-0.91840.7402-0.09480.05331.01230.04320.7394-1.9402-5.742-79.7675
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 19 )
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 51 )
3X-RAY DIFFRACTION3chain 'A' and (resid 52 through 104 )
4X-RAY DIFFRACTION4chain 'A' and (resid 105 through 149 )
5X-RAY DIFFRACTION5chain 'A' and (resid 150 through 210 )
6X-RAY DIFFRACTION6chain 'A' and (resid 211 through 224 )
7X-RAY DIFFRACTION7chain 'B' and (resid 4 through 33 )
8X-RAY DIFFRACTION8chain 'B' and (resid 34 through 51 )
9X-RAY DIFFRACTION9chain 'B' and (resid 52 through 72 )
10X-RAY DIFFRACTION10chain 'B' and (resid 73 through 135 )
11X-RAY DIFFRACTION11chain 'B' and (resid 136 through 149 )
12X-RAY DIFFRACTION12chain 'B' and (resid 150 through 200 )
13X-RAY DIFFRACTION13chain 'B' and (resid 201 through 219 )
14X-RAY DIFFRACTION14chain 'C' and (resid 4 through 19 )
15X-RAY DIFFRACTION15chain 'C' and (resid 20 through 51 )
16X-RAY DIFFRACTION16chain 'C' and (resid 52 through 104 )
17X-RAY DIFFRACTION17chain 'C' and (resid 105 through 119 )
18X-RAY DIFFRACTION18chain 'C' and (resid 120 through 135 )
19X-RAY DIFFRACTION19chain 'C' and (resid 136 through 148 )
20X-RAY DIFFRACTION20chain 'C' and (resid 149 through 201 )
21X-RAY DIFFRACTION21chain 'C' and (resid 202 through 216 )
22X-RAY DIFFRACTION22chain 'D' and (resid 1 through 19 )
23X-RAY DIFFRACTION23chain 'D' and (resid 20 through 33 )
24X-RAY DIFFRACTION24chain 'D' and (resid 34 through 64 )
25X-RAY DIFFRACTION25chain 'D' and (resid 65 through 104 )
26X-RAY DIFFRACTION26chain 'D' and (resid 105 through 135 )
27X-RAY DIFFRACTION27chain 'D' and (resid 136 through 216 )
28X-RAY DIFFRACTION28chain 'E' and (resid 3 through 19 )
29X-RAY DIFFRACTION29chain 'E' and (resid 20 through 51 )
30X-RAY DIFFRACTION30chain 'E' and (resid 52 through 72 )
31X-RAY DIFFRACTION31chain 'E' and (resid 73 through 166 )
32X-RAY DIFFRACTION32chain 'E' and (resid 167 through 201 )
33X-RAY DIFFRACTION33chain 'E' and (resid 202 through 219 )
34X-RAY DIFFRACTION34chain 'F' and (resid 4 through 33 )
35X-RAY DIFFRACTION35chain 'F' and (resid 34 through 51 )
36X-RAY DIFFRACTION36chain 'F' and (resid 52 through 72 )
37X-RAY DIFFRACTION37chain 'F' and (resid 73 through 104 )
38X-RAY DIFFRACTION38chain 'F' and (resid 105 through 119 )
39X-RAY DIFFRACTION39chain 'F' and (resid 120 through 135 )
40X-RAY DIFFRACTION40chain 'F' and (resid 136 through 149 )
41X-RAY DIFFRACTION41chain 'F' and (resid 150 through 166 )
42X-RAY DIFFRACTION42chain 'F' and (resid 167 through 210 )
43X-RAY DIFFRACTION43chain 'F' and (resid 211 through 224 )

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