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- PDB-3utd: Ec_IspH in complex with 4-oxopentyl diphosphate -

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Basic information

Entry
Database: PDB / ID: 3utd
TitleEc_IspH in complex with 4-oxopentyl diphosphate
Components4-hydroxy-3-methylbut-2-enyl diphosphate reductase
KeywordsOXIDOREDUCTASE / iron-sulfur protein / IspH / LytB / isoprenoid biosynthesis / non-mevalonate pathway
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-enyl diphosphate reductase activity / dimethylallyl diphosphate biosynthetic process / terpenoid biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / 3 iron, 4 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / metal ion binding / cytosol
Similarity search - Function
4-hydroxy-3-methylbut-2-enyl diphosphate reductase / LytB protein / 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
4-oxopentyl trihydrogen diphosphate / FE3-S4 CLUSTER / 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSpan, I. / Wang, K. / Wang, W. / Zhang, Y. / Bacher, A. / Eisenreich, W. / Schulz, C. / Oldfield, E. / Groll, M.
CitationJournal: Nat Commun / Year: 2012
Title: Discovery of acetylene hydratase activity of the iron-sulphur protein IspH.
Authors: Span, I. / Wang, K. / Wang, W. / Zhang, Y. / Bacher, A. / Eisenreich, W. / Li, K. / Schulz, C. / Oldfield, E. / Groll, M.
History
DepositionNov 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references
Revision 1.2Sep 13, 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_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details / _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: 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)72,6976
Polymers71,5812
Non-polymers1,1164
Water9,278515
1
A: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3483
Polymers35,7911
Non-polymers5582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3483
Polymers35,7911
Non-polymers5582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.110, 80.390, 111.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999699, 0.010469, 0.022178), (0.010756, 0.999859, 0.012867), (-0.02204, 0.013102, -0.999671)-65.72273, 0.38933, -0.55848

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Components

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


Mass: 35790.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ispH, lytB, yaaE, b0029, JW0027 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 blue / References: UniProt: P62623, EC: 1.17.1.2
#2: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4
#3: Chemical ChemComp-0CJ / 4-oxopentyl trihydrogen diphosphate


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


Mass: 18.015 Da / Num. of mol.: 515 / 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: 2.19 Å3/Da / Density % sol: 43.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M BIS-TRIS, 0.2 M ammonia sulfate, 25% PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING 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 13, 2011
RadiationMonochromator: double-crystal fixed-exit monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. all: 69488 / Num. obs: 69837 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 16.5
Reflection shellResolution: 1.7→1.8 Å / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 3.4 / % possible all: 99.8

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Processing

Software
NameVersionClassification
RemDAqdata collection
REFMAC5.5.0072refinement
AC5.5.0072refinement
XDSdata reduction
XSCALEdata scaling
REFMAC5.5.0072phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KE8
Resolution: 1.7→47.73 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.222 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20607 3476 5 %RANDOM
Rwork0.14583 ---
obs0.14884 66045 99.55 %-
all-69521 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å20 Å2
2---1.52 Å20 Å2
3---1.05 Å2
Refinement stepCycle: LAST / Resolution: 1.7→47.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4773 0 44 515 5332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0194897
X-RAY DIFFRACTIONr_bond_other_d0.0030.0224
X-RAY DIFFRACTIONr_angle_refined_deg2.0431.9756630
X-RAY DIFFRACTIONr_angle_other_deg0.707348
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5765617
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.24624.159226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.42615853
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0311544
X-RAY DIFFRACTIONr_chiral_restr0.1890.2762
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213672
X-RAY DIFFRACTIONr_rigid_bond_restr7.83634891
X-RAY DIFFRACTIONr_sphericity_free26.0715127
X-RAY DIFFRACTIONr_sphericity_bonded12.92355201
LS refinement shellResolution: 1.7→1.743 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 238 -
Rwork0.175 4415 -
obs--99.76 %
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)
13.1238-0.80030.18880.79640.40270.3585-0.010.04580.05040.10250.0602-0.09660.07150.0436-0.05020.07360.0104-0.00890.090.02160.0947-8.7024-7.9942-7.2163
21.95110.80870.47820.5170.04760.24720.1109-0.1055-0.0958-0.0428-0.0702-0.03840.1012-0.0189-0.04070.07860.0048-0.00360.09280.00050.0649-29.6223-10.1766-10.8962
32.006-0.2439-0.3160.17280.27170.5040.10880.1096-0.0322-0.0088-0.12380.0380.0492-0.12040.01510.11820.0281-0.06430.1398-0.04410.0454-39.9138-13.3159-21.8903
42.3222-0.2660.03551.55161.03960.7168-0.00090.067-0.0843-0.07570.0557-0.0631-0.05070.0477-0.05490.08760.01450.00440.0815-0.0170.0436-26.473-10.0486-21.5943
52.4868-1.61241.26341.7239-0.29391.0527-0.06910.2730.02450.0293-0.03990.0867-0.05810.22650.1090.07710.0219-0.0420.1141-0.01620.0627-36.9619-9.3555-27.7138
60.45670.56970.14290.72490.23470.37380.0220.01270.0077-0.0005-0.0040.0147-0.0197-0.0624-0.0180.09720.0326-0.03710.1048-0.02360.0602-40.8536-4.5668-20.7766
70.35471.93940.051411.4202-1.80175.7134-0.06570.03720.238-0.33610.31961.3491-0.0174-0.1635-0.25390.03070.0268-0.0750.0957-0.00440.2402-48.1852-0.1579-22.9417
80.48390.3699-0.36240.2994-0.27770.27390.0120.02720.02540.0150.00670.05380.0017-0.0085-0.01870.07780.0067-0.00420.0943-0.01250.0836-38.9661-0.5693-11.7502
92.3829-1.28690.15554.9824-0.32551.08390.0963-0.12050.06760.37260.06160.5054-0.0327-0.0763-0.15780.05270.01540.05440.072-0.01850.1349-43.916615.2868-8.894
100.7658-0.7819-0.55491.80220.56330.40230.03250.00970.0603-0.1020.00960.0192-0.0253-0.0091-0.04210.09170.0157-0.00340.06730.00080.053-31.032912.0297-17.2373
110.60730.2365-0.05451.4366-0.11320.34210.01850.08530.049-0.0565-0.04260.1145-0.1151-0.0310.02410.0790.0354-0.00590.0540.00660.0648-34.624320.9221-16.2243
120.18820.22770.16120.89510.0890.25290.00040.03990.00940.0424-0.0081-0.0486-0.02920.00540.00770.07740.00440.01070.0655-0.00720.0669-24.211114.3124-9.9623
132.6005-0.51130.62633.1393-1.58230.8516-0.0664-0.03960.18810.25290.06880.0731-0.1278-0.0374-0.00240.18220.00960.0120.0381-0.03010.042-29.403622.7495-5.2753
140.1682-0.0118-0.17460.0075-0.00780.4360.0285-0.09070.0377-0.00150.0082-0.01970.04050.0028-0.03670.085-0.0187-0.00170.1002-0.00160.0667-19.37212.9435-5.5365
150.96450.19480.27560.49110.46680.53910.0080.0044-0.0052-0.07050.0199-0.1078-0.0328-0.0215-0.02790.0631-0.00280.03220.0678-0.00590.1042-11.32690.5039-15.4248
160.6740.48710.52631.0977-0.08553.4069-0.1350.0106-0.0839-0.20550.0646-0.20520.03880.21720.07040.05060.0140.04460.0875-0.01470.1116-2.375-8.3947-20.2573
170.8889-0.09290.15170.1383-0.08170.0690.022-0.0771-0.0653-0.0496-0.0035-0.03240.022-0.0132-0.01850.06950.01060.00670.06510.00470.1011-14.658-11.5758-13.3768
181.7473-0.7156-0.86171.4661.3571.5156-0.0005-0.1068-0.14160.18740.1081-0.18380.2184-0.0205-0.10760.06990.0049-0.00450.10450.00870.0921-7.5483-11.7749-7.3067
195.45590.06852.63230.05590.30322.6137-0.0866-0.186-0.1280.008-0.0020.02670.037-0.10250.08860.0866-0.00810.00280.08560.01220.0543-31.6043-7.4973-2.1407
206.47890.6824-1.060513.75441.20368.666-0.151-0.09330.23070.642-0.35740.64880.4396-0.57620.50840.061-0.06310.0410.1237-0.05960.0822-43.9446-13.8208-8.026
214.20581.11580.15120.9579-0.44030.3621-0.0441-0.02760.1333-0.13230.08490.13440.0734-0.0512-0.04090.081-0.0153-0.02970.0795-0.01490.1339-56.8828-7.99137.8092
220.8534-0.47360.23840.6263-0.38260.28390.05850.0067-0.0280.0025-0.02160.04140.05550.0136-0.03690.0992-0.0033-0.00430.06760.00330.0475-33.6973-11.30217.7765
2312.9816-0.7583-2.51053.13350.86940.9650.2886-0.1699-0.27050.0788-0.0251-0.3218-0.0041-0.1705-0.26350.0974-0.0368-0.04270.13030.15020.2063-33.7149-18.049125.4275
240.1663-0.00640.33260.63580.03970.68670.0270.01860.01840.0368-0.025-0.08420.06340.0441-0.0020.067-0.004-0.01990.0946-0.01090.0708-24.872-6.061424.858
250.8857-2.50410.53367.2279-2.10482.8164-0.08160.04240.17920.2538-0.1348-0.5102-0.17370.11680.21640.0283-0.0236-0.05330.08980.00810.1289-18.22321.891121.0305
260.0183-0.00360.10320.3119-0.03120.62710.01410.01010.0046-0.0356-0.0146-0.06830.06690.02250.00050.07-0.00160.0030.1005-0.00060.0563-23.1326-4.36515.7804
272.4866-1.2337-1.52863.96232.01171.40970.30610.07370.4271-0.16590.0174-0.3787-0.1842-0.0325-0.32350.0863-0.01110.03790.07820.0220.1333-23.343912.07718.9241
280.04850.2497-0.07222.6362-0.07040.1753-0.0173-0.00110.0090.03780.0668-0.13710.05580.0154-0.04950.0694-0.00870.0070.0744-0.00490.0733-32.766813.149716.8057
290.36910.2133-0.50211.26290.42071.1654-0.055-0.0925-0.0189-0.08840.1056-0.23250.07240.1833-0.05060.0429-0.0278-0.00060.0964-0.03780.1845-23.334314.706617.9475
300.33390.08860.07381.56190.08590.44290.0177-0.0490.0448-0.036-0.03380.0321-0.05860.02330.01610.0704-0.01210.02260.0552-0.00260.0661-37.2519.701213.5508
312.5808-0.37010.22163.63922.38091.6426-0.01040.00920.1507-0.222-0.0161-0.0045-0.1449-0.01070.02650.1551-0.00890.02570.03740.03120.0433-35.805922.77435.5247
320.42560.2424-0.15160.73240.50210.6445-0.01010.02670.0427-0.0147-0.00430.06140.0123-0.00910.01440.08520.0127-0.00540.07820.00420.0687-44.01583.21426.0318
337.44051.5325-4.2012.962-4.62847.75080.21240.16840.19680.00040.0770.2323-0.0542-0.1368-0.28930.00620.00080.00460.0532-0.01190.2629-60.35610.3027.8057
340.81280.0802-0.13340.0785-0.14720.40820.0139-0.04350.07270.0605-0.02650.0588-0.06680.09350.01270.09240.00310.07490.0584-0.00360.1585-49.25350.359517.3092
350.4037-0.6507-0.26692.85380.12750.4167-0.0123-0.0780.04870.3306-0.00870.2619-0.06060.03860.0210.0557-0.01270.0510.0625-0.02640.1609-56.572-0.441218.1376
364.4915-0.89152.19931.3163-1.52995.9884-0.1044-0.24930.09130.2463-0.09020.44040.271-0.29710.19460.1221-0.06450.17120.0757-0.09040.2914-64.0841-8.198820.8569
370.7009-0.13550.14630.60290.24760.1685-0.01160.1194-0.05090.111500.10930.0490.04660.01160.0632-0.01110.01620.0579-0.01220.1235-50.8906-11.500513.788
382.48760.9252-1.60362.136-1.81392.4112-0.11610.2077-0.2199-0.23310.13210.24690.3178-0.0517-0.01590.0649-0.0180.01160.0893-0.03320.1195-57.9307-11.67627.784
395.3508-1.24692.38240.526-1.04142.1243-0.09660.2028-0.1412-0.00880.0012-0.02540.070.06930.09540.09780.02460.01680.11370.01060.0522-32.9919-7.90333.0504
4014.5849-0.98780.568416.2852-2.797814.61390.10270.93160.0536-0.1377-0.5645-0.78850.97380.44070.46190.10950.08440.03680.14440.04470.0472-22.6343-15.99667.8273
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 - 127
29X-RAY DIFFRACTION29B128 - 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 - 310

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