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- PDB-5jla: Crystal Structure of Ribose-5-phosphate Isomerase from Brucella m... -

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Basic information

Entry
Database: PDB / ID: 5jla
TitleCrystal Structure of Ribose-5-phosphate Isomerase from Brucella melitensis 16M
ComponentsPutative short-chain dehydrogenase/reductaseShort-chain dehydrogenase
KeywordsISOMERASE / alpha-beta-alpha / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Putative short-chain dehydrogenase/reductase
Similarity search - Component
Biological speciesBurkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / SSGCID / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of putative short-chain dehdrogenase/reductase from Burkholderia xenovorans LB400 bound to NAD
Authors: SSGCID / Delker, S.L. / Abendroth, J. / Lorimer, D. / Edwards, T.E.
History
DepositionApr 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative short-chain dehydrogenase/reductase
B: Putative short-chain dehydrogenase/reductase
C: Putative short-chain dehydrogenase/reductase
D: Putative short-chain dehydrogenase/reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,9348
Polymers113,2804
Non-polymers2,6544
Water18,3751020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19640 Å2
ΔGint-117 kcal/mol
Surface area30910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.480, 109.960, 64.990
Angle α, β, γ (deg.)90.000, 93.900, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Putative short-chain dehydrogenase/reductase / Short-chain dehydrogenase


Mass: 28320.033 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia xenovorans (strain LB400) (bacteria)
Strain: LB400 / Gene: Bxe_C0850 / Plasmid: BuxeA.00010.g.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13GR0
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1020 / 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: 1.99 Å3/Da / Density % sol: 38.2 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MCSG-1 c6(269929c6): 30% PPG P400, 0.2M MgCl, 0.1M Hepes, pH=7.5; cryo: direct; BuxeA.00010.g.B1.ps02594 at 7.5 mg/ml, puck rpa3-9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 3, 2016 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.45→41.934 Å / Num. obs: 154161 / % possible obs: 98.6 % / Redundancy: 4.85 % / Net I/σ(I): 10.67

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIXdev_2356refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3awd

3awd


Resolution: 1.45→41.934 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.1
RfactorNum. reflection% reflection
Rfree0.2363 2095 1.36 %
Rwork0.2062 --
obs0.2066 153836 98.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 62.71 Å2 / Biso mean: 18.4934 Å2 / Biso min: 3.14 Å2
Refinement stepCycle: final / Resolution: 1.45→41.934 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7292 0 176 1037 8505
Biso mean--20.91 29.09 -
Num. residues----1032
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077706
X-RAY DIFFRACTIONf_angle_d0.95910571
X-RAY DIFFRACTIONf_chiral_restr0.0811264
X-RAY DIFFRACTIONf_plane_restr0.0061375
X-RAY DIFFRACTIONf_dihedral_angle_d16.7452693
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.45-1.48380.38591090.3159557966693
1.4838-1.52090.27711320.25021025810390100
1.5209-1.5620.22391490.22261016910318100
1.562-1.6080.23871430.2081023710380100
1.608-1.65990.26731410.20651023510376100
1.6599-1.71920.24961620.20451021810380100
1.7192-1.7880.23831300.20821021410344100
1.788-1.86940.28761330.22102161034999
1.8694-1.9680.29451300.26029640977094
1.968-2.09130.24431480.208102091035799
2.0913-2.25270.22261250.215799681009397
2.2527-2.47940.24951320.2031100271015997
2.4794-2.83810.22631480.19561025610404100
2.8381-3.57540.20441590.1824102511041099
3.5754-41.95160.21451540.1835102861044099
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)
13.1138-0.84450.81783.8825-3.195.9865-0.05380.1992-0.1452-0.2571-0.0208-0.0530.23870.14960.06470.1043-0.0484-0.0020.046-0.00680.0965-47.3097-10.474113.3799
23.47010.64360.28072.63351.31762.00840.00610.1863-0.256-0.34570.0340.42640.0642-0.148-0.06290.1679-0.0512-0.00770.11320.0240.1426-57.739-8.323411.152
30.79520.01820.02083.4178-1.76861.7007-0.04330.05950.0345-0.16450.07210.16050.0943-0.1166-0.04840.1233-0.022-0.01860.08730.00120.0768-56.78472.574213.9616
41.04940.0898-0.13351.6098-0.60910.6818-0.0278-0.019-0.03880.0280.04760.1389-0.0014-0.0677-0.02870.0984-0.01330.00470.0699-0.0010.0767-51.41267.642615.9651
51.2675-0.4011.16651.5191-1.26993.8041-0.0127-0.0438-0.050.02350.07150.0664-0.04060.0449-0.06260.09880.01480.02950.04160.0060.0841-46.31659.235921.5605
61.5408-0.1114-0.03581.51770.1362.3868-0.00310.43390.0409-0.43630.30670.30140.1425-0.5026-0.16860.2304-0.0728-0.03770.21320.03850.1198-44.40532.19217.0654
70.76890.3787-0.5341.1609-0.61961.7175-0.11240.2921-0.0337-0.45340.17890.05520.209-0.2101-0.08310.198-0.0445-0.00120.1598-0.00610.0914-38.2220.73751.6208
81.5015-0.3766-0.31721.47020.46062.6262-0.001-0.0753-0.04270.08560.1405-0.0192-0.14490.0907-0.12580.0563-0.00610.00410.044-0.01590.0632-36.29420.349617.6683
93.83060.0284-0.45841.3152-0.54012.2404-0.13950.2926-0.1032-0.2940.1597-0.06290.2716-0.1011-0.0460.1494-0.00010.03160.0902-0.02320.0907-26.568612.3112-1.7662
103.51940.38450.76322.27761.45962.7331-0.0079-0.0547-0.21250.10320.0189-0.03070.17770.0413-0.02670.12580.04570.02580.05520.00360.135-20.3541-10.165918.7942
112.804-0.3160.28241.6007-0.01081.2375-0.0358-0.2112-0.39890.25680.0838-0.31970.14040.1742-0.08110.17320.07380.00890.1397-0.01440.239-9.9806-8.896920.7518
120.6449-0.1376-0.07421.72960.14680.4156-0.0175-0.0016-0.04570.05480.0905-0.32260.09450.1158-0.08160.10340.01730.00780.1057-0.02750.1721-10.98684.844216.6287
130.7322-0.1417-0.36821.11630.24061.4565-0.0494-0.0342-0.01940.03980.0543-0.15460.10720.1011-0.02410.09280.01260.01130.0662-0.01670.0968-21.98956.447418.5898
140.9115-0.1983-0.41.46670.4581.7874-0.0516-0.129-0.05140.21050.0196-0.03210.07150.06320.02670.10550.00480.00250.07670.01060.0749-32.18134.034327.7084
153.9825-1.0129-0.4984.48382.71564.1460.02630.14830.211-0.2604-0.027-0.0979-0.29120.0579-0.02260.1329-0.04740.00710.0549-0.00320.1282-20.110942.849315.3285
164.24210.54470.16792.3973-0.62971.5916-0.17320.22070.3593-0.27310.1135-0.4418-0.16340.23240.00750.1734-0.07560.0180.1478-0.05470.2274-9.489641.550314.8206
170.4821-0.01110.05961.11180.10720.4537-0.02320.0090.0413-0.02910.0712-0.2633-0.08610.1022-0.05320.1132-0.00680.01650.0927-0.02740.133-16.371426.968617.0003
182.62740.5680.29532.33820.5232.65850.01530.26880.0281-0.2607-0.0346-0.3291-0.0620.24140.00460.204-0.02050.04410.16920.01570.1046-25.969927.6935-4.4622
190.91390.41690.53411.76321.14531.8402-0.06380.04910.0541-0.13470.0462-0.0033-0.05560.0160.03670.07490.00560.0150.05680.00910.0713-32.539729.69129.6901
203.88220.8839-0.75342.9545-1.52154.9958-0.0286-0.21970.24010.22970.04440.1096-0.28610.1211-0.03880.09620.03740.02550.05140.00270.1143-47.558943.173717.0674
213.1428-0.12930.09361.62711.09281.8285-0.0501-0.22010.32280.23410.11570.5161-0.0877-0.1673-0.04610.13050.05580.04310.12480.03720.1991-58.176441.227518.1343
220.92860.0745-0.1023.2853-1.13810.7795-0.0085-0.0165-0.00390.10580.13510.291-0.0172-0.1179-0.14790.10730.00850.02620.10220.01710.1043-56.794330.125715.245
233.83411.3253-0.63927.5346-2.32531.9923-0.0454-0.1524-0.04270.2230.19320.4279-0.0114-0.173-0.11190.12240.02560.02470.10830.02150.1505-58.362518.709920.3497
243.05881.1806-1.10563.4212-1.20592.1516-0.00780.21350.0997-0.22360.04940.1281-0.1134-0.0755-0.09030.1280.0103-0.01520.10860.03090.1202-53.258230.66844.7613
250.96960.1172-0.31351.6147-0.61841.4071-0.01430.01680.0154-0.01710.05220.0913-0.0009-0.0666-0.04030.06450.00310.00470.04810.00050.0605-45.251123.977213.2117
261.46230.0267-0.50461.34030.31482.4723-0.0302-0.3427-0.010.39050.33050.3809-0.2182-0.6122-0.1240.19610.10740.07670.24570.05870.1394-45.827830.393924.251
273.1558-1.84710.76522.0860.43032.7423-0.0679-0.4196-0.14740.45650.10530.30140.0295-0.4073-0.06780.25360.03540.04380.22260.00340.1189-40.950427.726636.7844
280.88040.03460.19911.0947-0.90323.5688-0.0153-0.03910.08970.1070.05240.0265-0.0814-0.044-0.05160.06860.0110.01090.0581-0.00640.0809-37.786934.503716.76
294.8873-0.24391.60571.0685-1.69753.1812-0.1092-0.2473-0.01180.14720.0568-0.0279-0.1872-0.06630.02830.17560.01830.00620.1022-0.01430.0997-29.072420.383534.865
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 31 )A3 - 31
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 64 )A32 - 64
3X-RAY DIFFRACTION3chain 'A' and (resid 65 through 102 )A65 - 102
4X-RAY DIFFRACTION4chain 'A' and (resid 103 through 152 )A103 - 152
5X-RAY DIFFRACTION5chain 'A' and (resid 153 through 174 )A153 - 174
6X-RAY DIFFRACTION6chain 'A' and (resid 175 through 195 )A175 - 195
7X-RAY DIFFRACTION7chain 'A' and (resid 196 through 228 )A196 - 228
8X-RAY DIFFRACTION8chain 'A' and (resid 229 through 245 )A229 - 245
9X-RAY DIFFRACTION9chain 'A' and (resid 246 through 261 )A246 - 261
10X-RAY DIFFRACTION10chain 'B' and (resid 3 through 31 )B3 - 31
11X-RAY DIFFRACTION11chain 'B' and (resid 32 through 64 )B32 - 64
12X-RAY DIFFRACTION12chain 'B' and (resid 65 through 131 )B65 - 131
13X-RAY DIFFRACTION13chain 'B' and (resid 132 through 196 )B132 - 196
14X-RAY DIFFRACTION14chain 'B' and (resid 197 through 260 )B197 - 260
15X-RAY DIFFRACTION15chain 'C' and (resid 3 through 31 )C3 - 31
16X-RAY DIFFRACTION16chain 'C' and (resid 32 through 64 )C32 - 64
17X-RAY DIFFRACTION17chain 'C' and (resid 65 through 196 )C65 - 196
18X-RAY DIFFRACTION18chain 'C' and (resid 197 through 216 )C197 - 216
19X-RAY DIFFRACTION19chain 'C' and (resid 217 through 260 )C217 - 260
20X-RAY DIFFRACTION20chain 'D' and (resid 3 through 31 )D3 - 31
21X-RAY DIFFRACTION21chain 'D' and (resid 32 through 64 )D32 - 64
22X-RAY DIFFRACTION22chain 'D' and (resid 65 through 102 )D65 - 102
23X-RAY DIFFRACTION23chain 'D' and (resid 103 through 114 )D103 - 114
24X-RAY DIFFRACTION24chain 'D' and (resid 115 through 131 )D115 - 131
25X-RAY DIFFRACTION25chain 'D' and (resid 132 through 174 )D132 - 174
26X-RAY DIFFRACTION26chain 'D' and (resid 175 through 196 )D175 - 196
27X-RAY DIFFRACTION27chain 'D' and (resid 197 through 216 )D197 - 216
28X-RAY DIFFRACTION28chain 'D' and (resid 217 through 245 )D217 - 245
29X-RAY DIFFRACTION29chain 'D' and (resid 246 through 261 )D246 - 261

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