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- PDB-3uv3: Ec_IspH in complex with but-2-ynyl diphosphate (1086) -

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Basic information

Entry
Database: PDB / ID: 3uv3
TitleEc_IspH in complex with but-2-ynyl diphosphate (1086)
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 / 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
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
but-2-yn-1-yl trihydrogen diphosphate / IRON/SULFUR CLUSTER / 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 29, 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_comp_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_comp_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_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_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)72,7446
Polymers71,5812
Non-polymers1,1634
Water7,188399
1
A: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3723
Polymers35,7911
Non-polymers5822
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)36,3723
Polymers35,7911
Non-polymers5822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.230, 80.400, 111.950
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(-0.999773, 0.009771, 0.018951), (0.00993, 0.999916, 0.008271), (-0.018868, 0.008457, -0.999786)-65.82266, 0.3236, -0.34464

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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, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-0CM / but-2-yn-1-yl trihydrogen diphosphate


Mass: 230.050 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O7P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 399 / 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: 2.21 Å3/Da / Density % sol: 44.29 %
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: May 23, 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: 1.6→40 Å / Num. all: 84172 / Num. obs: 81563 / % possible obs: 96.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 14.6
Reflection shellResolution: 1.6→1.7 Å / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 2.6 / % possible all: 91.5

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Processing

Software
NameVersionClassification
RemDAqdata collection
REFMAC5.5.0072refinement
XDSdata reduction
XSCALEdata scaling
REFMAC5.5.0072phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KE8
Resolution: 1.6→40 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.509 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22057 4079 5 %RANDOM
Rwork0.16716 ---
obs0.16986 77483 96.87 %-
all-81562 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.117 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2---1.84 Å20 Å2
3---1.51 Å2
Refinement stepCycle: LAST / Resolution: 1.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4773 0 42 399 5214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0194899
X-RAY DIFFRACTIONr_angle_refined_deg2.1331.9766642
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5375617
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.93524.159226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.44715853
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4151544
X-RAY DIFFRACTIONr_chiral_restr0.1850.2764
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213664
X-RAY DIFFRACTIONr_rigid_bond_restr7.63734875
X-RAY DIFFRACTIONr_sphericity_free21.4925118
X-RAY DIFFRACTIONr_sphericity_bonded11.61755072
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 249 -
Rwork0.227 4746 -
obs--87.07 %
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)
12.6834-0.2446-0.03280.30970.28780.28730.013-0.1421-0.13130.05060.0422-0.05060.05850.0114-0.05510.10380.0057-0.00370.08470.01450.0888-9.1205-7.9185-7.3301
22.51670.33391.02490.89270.02940.43130.1578-0.086-0.1892-0.0563-0.0757-0.01850.0733-0.0212-0.08210.0972-0.0011-0.00720.1042-0.00640.0554-29.7068-10.1849-10.8823
34.36940.14960.0850.48190.67210.98710.25630.2727-0.1610.0144-0.1794-0.01970.0547-0.1976-0.07690.1150.0461-0.08490.1526-0.05080.072-39.9709-13.4183-21.9182
45.3175-0.38430.44570.1961-0.09170.05960.08170.1042-0.2518-0.0576-0.02590.09180.01610.0189-0.05580.11790.01890.01550.0963-0.0320.0765-26.5832-10.0774-21.5307
54.1449-2.86641.71783.9246-0.33381.103-0.00950.3680.0185-0.138-0.0248-0.0287-0.0810.21630.03430.10390.0253-0.03430.1603-0.05110.0681-37.0454-9.4523-27.7217
60.32460.5560.4471.00070.71821.02190.0235-0.06290.0352-0.0589-0.1020.0798-0.0058-0.14920.07850.17110.0356-0.0510.1154-0.03280.0667-41.0174-4.7405-20.841
72.05432.205-0.17714.18150.2412.0099-0.0653-0.00650.1832-0.2681-0.00960.6578-0.0302-0.2140.07490.06510.0548-0.10010.1137-0.04620.1895-48.3709-0.272-22.9385
80.8596-0.0141-0.01240.2773-0.39760.58770.03990.0121-0.02610.02950.00740.055-0.0231-0.0252-0.04730.0852-0.00080.00570.107-0.02140.0933-39.0977-0.6491-11.7704
93.1339-2.7675-0.24778.4857-0.97321.57940.1363-0.1995-0.13120.41330.06790.8329-0.1161-0.1387-0.20420.07340.00960.0660.0969-0.02210.1712-43.943815.3085-8.8925
100.8603-1.2008-0.35053.21530.68530.46640.00740.01360.037-0.10580.01010.1-0.04470.0212-0.01750.09790.0182-0.00120.07390.00020.0578-31.107911.9368-17.1914
110.88770.37220.26071.685-0.16990.4575-0.0060.1320.0512-0.0805-0.03240.1699-0.1691-0.01490.03850.11670.0473-0.01190.04890.00560.0764-34.703120.8569-16.2731
120.20510.5040.01151.4574-0.07810.08730.01250.0159-0.04090.05390.0004-0.061-0.0604-0.0115-0.01290.10970.00920.00790.0739-0.0110.0652-24.300114.2928-9.9638
132.5405-0.31880.46963.9627-2.19821.25350.07020.0270.1170.24-0.03630.1029-0.11990.0279-0.03390.22440.020.01120.05-0.03950.0424-29.477322.7586-5.2961
140.9149-0.30490.09880.27480.03610.04090.0123-0.05870.05550.0455-0.0023-0.03820.0158-0.003-0.010.1004-0.00240.00130.0981-0.00760.0579-19.45042.9078-5.5183
150.89520.11530.07370.55820.3340.34110.01970.02360.0386-0.0622-0.0092-0.130.0003-0.0561-0.01050.07230.00520.01860.07140.00760.0933-11.43960.4908-15.4609
160.8823-0.07780.04751.08150.00952.2625-0.00980.0946-0.1349-0.1430.0454-0.21950.0760.205-0.03560.03350.01810.04890.0742-0.01610.1249-2.5276-8.4042-20.3392
171.16180.07510.07170.03570.00940.00520.03230.0227-0.0501-0.0284-0.0206-0.051-0.0022-0.0032-0.01170.10110.01540.00790.07490.00820.1077-14.7258-11.6038-13.4241
182.6151-1.6938-1.46072.05832.58893.7920.0187-0.1868-0.08980.2080.1047-0.12580.3749-0.0134-0.12350.06490.0085-0.01360.0756-0.02590.1609-7.5767-11.8764-7.462
194.13040.29272.50190.11890.55252.9611-0.0366-0.3291-0.15220.01990.00030.01840.0879-0.14430.03630.1053-0.02050.00530.09560.01480.0669-31.6889-7.5354-2.0694
2010.1945-5.26-0.268212.859813.469417.5249-0.0139-0.4806-0.47980.3967-0.49690.61860.5153-0.99130.51070.0663-0.10260.01010.1922-0.01650.1155-43.9877-13.9106-8.0463
216.50571.3037-0.62591.5906-0.62810.4868-0.16760.2182-0.2251-0.20670.14880.33270.0464-0.03340.01880.1153-0.0085-0.04670.05880.00760.2236-56.5772-7.77367.866
220.6599-0.37480.28080.8603-0.39450.23830.06380.0186-0.0180.0391-0.01380.0490.04850.0087-0.050.1133-0.006-0.00850.07530.00390.0572-33.6914-11.238617.9826
235.1582-0.60880.54820.224-0.62762.19290.23920.0448-0.19980.00220.03630.0814-0.0195-0.1319-0.27550.1369-0.0231-0.05440.07730.00770.0647-33.8003-18.049125.5715
240.2292-0.02770.36440.45720.0070.58980.04330.02380.01220.0588-0.0394-0.04390.08290.0331-0.00380.1007-0.0075-0.02590.0948-0.00130.0651-24.8673-6.116425.1364
251.2357-2.17960.44716.7765-4.07393.8685-0.08060.06840.25310.2324-0.195-0.5693-0.1530.11570.27560.0409-0.0286-0.06540.08460.01720.1317-18.22061.940221.1141
260.6429-0.22950.53210.7967-0.20970.450.04930.01930.0296-0.1008-0.0586-0.12170.06970.00660.00930.10020.0062-0.0110.10440.00290.0695-23.1397-4.339415.9809
270.0395-0.2003-0.11846.6623.57841.93120.08920.03990.1029-0.1890.1828-0.4908-0.10070.0541-0.2720.16830.02280.13650.12040.10890.2904-23.43112.18849.0119
280.14460.5705-0.20823.6175-0.32450.48540.01230.0120.01120.13020.0671-0.16370.0039-0.0175-0.07940.0882-0.0154-0.00770.0809-0.00250.0805-32.851313.192516.8414
292.29331.8126-0.92653.0026-0.16430.58780.0214-0.22550.10430.05770.0711-0.15210.02420.1713-0.09240.0647-0.0354-0.02830.0864-0.02650.1977-23.433314.751718.0115
300.64780.02080.13971.9010.03320.30620.0071-0.04280.059-0.0183-0.01440.0131-0.04830.0040.00730.09-0.00910.01590.0535-0.00160.0785-37.331619.741613.5688
312.2308-0.14070.30732.41941.91871.6010.05860.02240.1282-0.1874-0.0484-0.0508-0.1323-0.0381-0.01020.19-0.00850.02940.03230.03520.0524-35.935922.76565.5258
320.47360.2023-0.14840.60980.08060.09120.00150.01880.0332-0.0651-0.01210.1164-0.00670.00430.01060.10550.0071-0.01240.09040.0070.0771-44.07173.23676.0524
3310.07694.1104-5.82612.5701-4.54268.97710.19850.36070.25110.0560.10330.3358-0.1382-0.1029-0.30180.02180.0134-0.08970.0234-0.03440.5117-60.41530.32217.8875
341.47790.27510.64990.8128-0.31890.55180.04810.0210.10620.2060.00130.2413-0.08670.0409-0.04940.11090.01640.07040.08080.02080.1446-49.31790.442917.3695
350.9194-1.0062-0.23651.3371-0.16951.7197-0.1059-0.1105-0.06210.25630.13830.2514-0.1444-0.0988-0.03250.10670.00170.12670.0383-0.00320.2475-56.6228-0.354818.1917
365.7828-2.67322.95323.5247-1.9888.9055-0.1997-0.31310.08330.5129-0.01240.77490.3485-0.61210.21210.1301-0.04970.18730.0891-0.04690.3686-64.0801-8.08121.0622
371.3823-0.15620.02270.44720.22050.1283-0.09370.016-0.08880.10180.05620.15970.03350.05240.03750.0864-0.0180.03670.0534-0.00810.1751-50.968-11.423913.9243
383.63672.6171-3.62924.8434-3.76586.0109-0.15070.2199-0.214-0.35070.08980.50770.4839-0.020.06080.06340.0031-0.01870.0568-0.04390.1892-58.0353-11.66327.9226
397.5542-1.8452.58740.7478-1.12881.747-0.11940.1863-0.0011-0.0322-0.0137-0.0620.09210.06570.13310.10440.02520.01160.11240.00540.0601-33.0597-7.89083.1451
4015.8295-6.6895-6.167330.681-11.001728.19010.18850.68970.1554-0.979-0.6855-0.7511.28950.39830.4970.14160.1190.04960.13340.0390.0244-22.7223-16.01227.9832
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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