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- PDB-3t0f: IspH:HMBPP (substrate) structure of the E126D mutant -

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Basic information

Entry
Database: PDB / ID: 3t0f
TitleIspH:HMBPP (substrate) structure of the E126D mutant
Components4-hydroxy-3-methylbut-2-enyl diphosphate reductase
KeywordsOXIDOREDUCTASE / 3Fe-4S iron-sulfur cluster / conserved cysteine / IPP and DMAPP production final step / non-mevalonate pathway / substrate HMBPP / low activity
Function / homology
Function and homology information


hydroxymethylbutenyl pyrophosphate reductase activity / 4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductase / 4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductase activity / dimethylallyl diphosphate biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / 3 iron, 4 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / metal ion binding / cytosol
Similarity search - Function
LytB protein / 4-hydroxy-3-methylbut-2-enyl diphosphate reductase / 4-hydroxy-3-methylbut-2-enyl diphosphate reductase, catalytic domain / Rossmann fold - #11270 / Cobalt-precorrin-4 Transmethylase; domain 1 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FE3-S4 CLUSTER / Chem-H6P / 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSpan, I. / Graewert, T. / Bacher, A. / Eisenreich, W. / Groll, M.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Crystal Structures of Mutant IspH Proteins Reveal a Rotation of the Substrate's Hydroxymethyl Group during Catalysis.
Authors: Span, I. / Grawert, T. / Bacher, A. / Eisenreich, W. / Groll, M.
History
DepositionJul 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Database references
Revision 1.2Feb 15, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
B: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5346
Polymers72,4182
Non-polymers1,1164
Water3,315184
1
A: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7673
Polymers36,2091
Non-polymers5582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7673
Polymers36,2091
Non-polymers5582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.850, 80.180, 114.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 309
2114B1 - 309

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Components

#1: Protein 4-hydroxy-3-methylbut-2-enyl diphosphate reductase / / IspH


Mass: 36209.004 Da / Num. of mol.: 2 / Mutation: E126D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ispH, lytB, yaaE, b0029, JW0027 / Production host: Escherichia coli (E. coli)
References: UniProt: P62623, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
#2: Chemical ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4
#3: Chemical ChemComp-H6P / (2E)-4-hydroxy-3-methylbut-2-en-1-yl trihydrogen diphosphate / (E)-4-Hydroxy-3-methyl-but-2-enyl pyrophosphate


Mass: 262.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O8P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.06 Å3/Da / Density % sol: 40.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 200 mM lithium sulfate, 25% PEG3350, 100 mM Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 11, 2011
RadiationMonochromator: Fixed-exit LN2 cooled Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 47801 / Num. obs: 47419 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.147 / Net I/σ(I): 9.3
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.558 / Mean I/σ(I) obs: 2.4 / % possible all: 97.4

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Processing

Software
NameClassification
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3F7T
Resolution: 1.9→10 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.91 / SU B: 8.213 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24215 2352 5 %RANDOM
Rwork0.20139 ---
obs0.20342 44686 100 %-
all-47038 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.716 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2---1.97 Å20 Å2
3---2.03 Å2
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4767 0 44 184 4995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0224890
X-RAY DIFFRACTIONr_angle_refined_deg2.3161.9686611
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7625612
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.01223.965227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.28315849
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4551544
X-RAY DIFFRACTIONr_chiral_restr0.1830.2758
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213658
X-RAY DIFFRACTIONr_mcbond_it1.3411.53063
X-RAY DIFFRACTIONr_mcangle_it2.11424934
X-RAY DIFFRACTIONr_scbond_it3.56331827
X-RAY DIFFRACTIONr_scangle_it5.4494.51665
X-RAY DIFFRACTIONr_rigid_bond_restr2.28134890
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2303 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.380.5
Amedium thermal2.542
Bmedium positional0.380.5
Bmedium thermal2.542
LS refinement shellResolution: 1.9→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 163 -
Rwork0.24 3113 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.30780.063-0.15531.2885-0.61230.3584-0.06440.1598-0.06370.16370.10380.1392-0.0292-0.0675-0.03950.17510.00260.02850.2206-0.01920.1075.3849.004-10.496
20.0486-0.0885-0.0970.56010.24540.2276-0.024-0.0376-0.0038-0.03350.00670.0162-0.00420.03760.01730.13930.005-0.00850.16050.00510.118128.902810.7953-11.3108
31.1552-0.22990.22630.12590.15630.57480.0621-0.02210.0125-0.0333-0.0078-0.0462-0.0499-0.0216-0.05430.1328-0.03070.01420.11950.00110.149140.680415.1899-21.0941
40.2463-0.05020.03420.55561.00952.08390.0479-0.105-0.018-0.0035-0.0213-0.0162-0.1037-0.0559-0.02650.11910.003-0.00810.14070.00460.135526.942311.4683-22.5952
52.6162-2.4265-0.94692.25870.90760.54580.02850.10410.0643-0.0183-0.0839-0.0575-0.0103-0.08550.05550.1452-0.00720.02560.121-0.010.133438.485312.0944-27.6178
60.5570.4321-0.69940.3946-0.46860.9715-0.03980.12880.0751-0.06560.16920.02280.003-0.0724-0.12950.160.00310.01630.1511-0.01980.129841.40985.778-20.6964
72.76541.0646-0.7824.5713-2.9461.9030.0333-0.1245-0.0241-0.1407-0.1695-0.21660.09220.12290.13620.11310.01920.05630.1486-0.02390.144149.0472.0558-21.8853
81.33680.0136-0.29370.2192-0.07780.69760.02370.0364-0.020.12050.0218-0.0954-0.0573-0.0591-0.04550.15580.003-0.01180.1346-0.00870.10738.35531.1201-12.2552
95.853-2.4623-1.69488.27452.76131.0719-0.0681-0.4982-0.14060.25420.071-0.12060.07080.1045-0.00290.1260.0042-0.02270.13580.02290.1543.3754-14.5827-10.2943
104.85990.3457-1.28260.19970.10870.574-0.12350.02840.2457-0.11290.11110.0605-0.09980.07360.01250.17930.0019-0.02590.1563-0.02210.112230.988-11.2513-20.0368
111.29470.9821-0.08341.9872-0.14030.2058-0.09240.0383-0.1514-0.13420.0233-0.19250.06980.0070.06910.1270.01870.02830.0905-0.01820.12134.7353-20.2456-18.5137
121.1091-0.10210.40962.1130.59890.5532-0.04850.0436-0.11170.02870.04850.0234-0.0656-0.004300.1114-0.00360.00320.1291-0.00110.117123.7906-13.6711-12.7408
134.49590.0044-0.79692.71732.14811.84160.2717-0.2282-0.25820.097-0.1364-0.23190.0191-0.0752-0.13540.18330.0038-0.03150.08170.04330.092629.3049-22.0116-7.4782
140.0307-0.13250.03560.5948-0.15680.0422-0.0034-0.0029-0.02580.06560.02220.0704-0.01150.0027-0.01880.1427-0.0032-0.00010.1309-0.0020.155318.6199-2.6355-8.377
151.25680.11680.14990.3143-0.25250.25760.08310.0089-0.1044-0.0281-0.00170.09350.03110.0212-0.08140.1364-0.0052-0.01960.1316-0.00340.148311.68760.2477-19.1088
164.06950.4537-1.05932.5428-0.21963.78960.08730.3860.0737-0.15540.12650.2909-0.061-0.1831-0.21380.07020.0084-0.05150.11230.01020.16233.35579.3823-24.3176
171.8577-0.71080.27530.2864-0.11940.0717-0.0224-0.07070.030.04490.03670.018-0.05770.0263-0.01430.1485-0.00490.00690.1353-0.00330.145914.36512.2769-15.7911
181.7167-2.06832.91392.5105-3.44895.8762-0.077-0.0563-0.02990.10430.06450.084-0.1453-0.12860.01250.0945-0.00840.02120.1151-0.00210.14166.975211.8574-10.3649
193.1783-0.3043-0.26040.0385-0.05630.7644-0.1166-0.2282-0.150.01680.0050.0067-0.06490.08430.11150.15260.00140.0010.1533-0.01720.099730.20517.2125-3.0093
2013.9394-3.7018-11.750322.8291.64328.92030.0271-0.5461-0.51440.5785-0.3554-0.9895-0.36470.84550.32820.0811-0.0628-0.06660.1450.04760.109542.894614.4438-6.9644
210.94880.66290.83191.74160.72170.7714-0.06710.0396-0.0875-0.13150.1028-0.0888-0.07260.0248-0.03580.18580.0060.01710.14480.00940.093757.2258.139.254
220.7707-0.3802-0.31410.4590.29270.22170.00070.02820.0233-0.0186-0.02670.0241-0.0150.00040.02590.13080.0010.00480.1341-0.00280.11230.686210.202816.7682
236.6044-3.45862.778714.19373.52993.18130.0238-0.32320.59140.0334-0.308-0.11180.047-0.29110.28420.1692-0.0080.04380.1739-0.07770.147229.559816.541224.1623
240.3411-0.5849-0.3261.10030.43980.6607-0.0028-0.0031-0.06220.02190.0210.0606-0.0093-0.1064-0.01820.1173-0.0170.02740.15560.02160.14221.14534.788123.2788
254.2435-4.447-4.848712.83513.05756.0496-0.12470.3473-0.48580.0503-0.33120.73580.1237-0.40360.45590.0973-0.08750.03270.1430.0120.224115.0691-3.221618.5518
261.3184-0.6216-0.7840.31860.46841.08420.1370.0061-0.1477-0.096-0.010.0541-0.1232-0.04-0.12710.1289-0.0093-0.00660.13370.0050.159820.51743.246713.7554
278.8087.1611-0.79945.9876-1.20663.5605-0.33250.34750.255-0.3260.43240.3004-0.3122-0.1716-0.09990.2414-0.0817-0.0670.23610.08270.19321.6304-12.70526.0371
280.73240.2428-2.13730.1226-0.82686.5697-0.0158-0.1106-0.15250.0497-0.01420.0883-0.16480.18210.030.11710.08570.09680.09150.16010.53229.4301-18.047212.4442
291.6058-2.4693-4.12923.87036.461310.78860.0853-0.1934-0.0451-0.0640.2481-0.235-0.11360.3967-0.33340.0531-0.0733-0.12880.11210.23671.341123.1033-13.473815.1217
301.2573-0.7719-0.30812.3303-0.23290.4416-0.0735-0.1038-0.39420.0720.05960.2979-0.03640.06630.01380.07980.01750.00330.09980.02250.249434.7519-20.672210.8308
314.1347-1.8872.89442.857-2.99413.43120.29890.3399-0.7664-0.2151-0.00170.07580.25390.1118-0.29720.19210.0508-0.08080.0657-0.10270.283934.2148-22.78372.4529
320.34320.25050.46160.24380.26420.71560.01920.0257-0.01830.02050.0004-0.0206-0.00550.0336-0.01960.12420.01190.01020.1416-0.00620.141442.0445-3.56075.7482
332.2595-1.953.36221.939-3.5936.9770.129-0.06180.0275-0.2276-0.0314-0.05380.50140.135-0.09760.07530.0090.01040.0727-0.03970.417758.0455-0.87629.2127
340.80270.01310.58110.00460.00980.42090.0134-0.042-0.02950.01450.0082-0.02220.0131-0.0346-0.02150.1560.0037-0.01850.12910.0060.157445.9607-1.366717.8296
350.5023-0.037-0.28122.85190.31270.18850.03530.0367-0.04030.0473-0.0237-0.2576-0.016-0.0334-0.01160.11570.0065-0.03650.13540.01470.154353.0154-0.560519.4075
360.79760.5664-1.68520.5352-1.21495.79440.0106-0.1196-0.1570.1326-0.1001-0.1499-0.03150.33530.08950.1175-0.0111-0.0350.17180.00460.118460.33946.656423.1938
370.34030.2925-0.31390.4196-0.48110.55680.00140.09040.05570.06340.03970.0441-0.091-0.031-0.0410.13450-0.0060.12980.00260.126648.020310.728114.8243
381.2131.32341.2851.76092.21993.5297-0.06430.04030.1456-0.0896-0.03040.1156-0.1438-0.08150.09480.10180.0081-0.02070.15150.0120.145355.630111.039.5202
395.8687-0.7665-0.8960.27280.44580.77510.00130.0995-0.0198-0.0446-0.0291-0.0004-0.1099-0.0490.02780.1370.0088-0.02020.15950.00970.091131.20357.50232.1601
4022.236413.62615.41621.7587-0.945418.7665-0.44610.7261.0031-0.17620.34171.462-0.43150.52490.10440.09320.0835-0.05820.2576-0.09880.20719.411614.46926.0706
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 7
2X-RAY DIFFRACTION2A8 - 24
3X-RAY DIFFRACTION3A25 - 37
4X-RAY DIFFRACTION4A38 - 49
5X-RAY DIFFRACTION5A50 - 64
6X-RAY DIFFRACTION6A65 - 77
7X-RAY DIFFRACTION7A78 - 89
8X-RAY DIFFRACTION8A90 - 103
9X-RAY DIFFRACTION9A104 - 114
10X-RAY DIFFRACTION10A115 - 127
11X-RAY DIFFRACTION11A128 - 162
12X-RAY DIFFRACTION12A163 - 181
13X-RAY DIFFRACTION13A182 - 193
14X-RAY DIFFRACTION14A194 - 210
15X-RAY DIFFRACTION15A211 - 246
16X-RAY DIFFRACTION16A247 - 261
17X-RAY DIFFRACTION17A262 - 280
18X-RAY DIFFRACTION18A281 - 297
19X-RAY DIFFRACTION19A298 - 304
20X-RAY DIFFRACTION20A305 - 309
21X-RAY DIFFRACTION21B1 - 7
22X-RAY DIFFRACTION22B8 - 49
23X-RAY DIFFRACTION23B50 - 54
24X-RAY DIFFRACTION24B55 - 76
25X-RAY DIFFRACTION25B77 - 86
26X-RAY DIFFRACTION26B87 - 100
27X-RAY DIFFRACTION27B101 - 112
28X-RAY DIFFRACTION28B113 - 122
29X-RAY DIFFRACTION29B129 - 140
30X-RAY DIFFRACTION30B141 - 181
31X-RAY DIFFRACTION31B182 - 193
32X-RAY DIFFRACTION32B194 - 207
33X-RAY DIFFRACTION33B208 - 216
34X-RAY DIFFRACTION34B217 - 235
35X-RAY DIFFRACTION35B236 - 248
36X-RAY DIFFRACTION36B249 - 261
37X-RAY DIFFRACTION37B262 - 280
38X-RAY DIFFRACTION38B281 - 297
39X-RAY DIFFRACTION39B298 - 305
40X-RAY DIFFRACTION40B306 - 309

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