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- PDB-3uwm: Ec_IspH in complex with 4-oxobutyl diphosphate (1302) -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 3uwm
TitleEc_IspH in complex with 4-oxobutyl diphosphate (1302)
Components4-hydroxy-3-methylbut-2-enyl diphosphate reductase
KeywordsOXIDOREDUCTASE / Cytosol / iron-sulfur protein / Reductase
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
Chem-0JX / 4-oxobutyl 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: 1.8 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
DepositionDec 2, 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_alt_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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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)73,2778
Polymers71,5812
Non-polymers1,6966
Water8,197455
1
A: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6384
Polymers35,7911
Non-polymers8483
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)36,6384
Polymers35,7911
Non-polymers8483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.660, 80.700, 111.790
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(-0.999895, 0.004811, 0.01364), (0.004861, 0.999982, 0.003642), (-0.013622, 0.003708, -0.9999)-66.01871, 0.16199, -0.47989

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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-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-0K2 / 4-oxobutyl trihydrogen diphosphate


Mass: 248.065 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O8P2
#4: Chemical ChemComp-0JX / (3E)-4-hydroxybut-3-en-1-yl trihydrogen diphosphate


Mass: 248.065 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O8P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 455 / 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: 2.23 Å3/Da / Density % sol: 44.75 %
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
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: 1.8→50 Å / Num. all: 59963 / Num. obs: 59603 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 10.9
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 4.2 / % possible all: 97.6

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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: 1.8→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.926 / SU B: 6.987 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.256 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26831 2981 5 %RANDOM
Rwork0.18459 ---
obs0.18875 56621 99.45 %-
all-59603 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.041 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2---2.21 Å20 Å2
3---2.09 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4773 0 72 455 5300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0194895
X-RAY DIFFRACTIONr_angle_refined_deg2.0841.9746626
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0915617
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.57524.159226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.75515853
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0021544
X-RAY DIFFRACTIONr_chiral_restr0.1450.2762
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213664
X-RAY DIFFRACTIONr_rigid_bond_restr5.86534895
X-RAY DIFFRACTIONr_sphericity_free29.9145132
X-RAY DIFFRACTIONr_sphericity_bonded19.34155138
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 198 -
Rwork0.178 3678 -
obs--95.02 %
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)
10.00920.01270.00540.01810.00710.00380.0145-0.0152-0.0230.01-0.0097-0.03660.0117-0.0094-0.00480.08710.001-0.00820.07310.00110.0935-12.2539-6.6686-9.2054
20.490.190.05820.07580.02210.00710.0098-0.0335-0.0269-0.0092-0.0097-0.00960.0038-0.0052-0.00010.07870.0013-0.00130.0689-0.00130.0803-29.8363-10.1741-11.0324
30.45590.6063-0.08271.1384-0.26570.13120.04120.0335-0.01530.004-0.03570.0194-0.01910.005-0.00540.07270.0057-0.00830.0734-0.0060.0801-40.2963-13.4078-21.8597
40.5662-0.13860.16790.1865-0.0660.41520.01350.018-0.07210.0136-0.0042-0.0032-0.0267-0.0012-0.00930.07540.0046-0.00240.0657-0.00070.0731-26.7853-10.2301-21.8343
50.8342-0.6716-0.0550.64450.14170.09640.04840.0525-0.0101-0.0522-0.0312-0.0216-0.0152-0.006-0.01730.08140.0103-0.00350.0832-0.00480.079-37.5153-9.507-27.73
60.16980.25160.10420.38990.19730.206-0.0165-0.00870.0163-0.0404-0.01190.0374-0.0034-0.00370.02840.07430.0069-0.00420.0724-0.0050.0829-41.1928-4.698-20.773
70.24680.62610.2531.740.88550.6528-0.017-0.00530.0067-0.0729-0.07790.0674-0.0757-0.1040.09490.07110.0099-0.02070.0716-0.01220.0922-48.5668-0.1263-22.6684
80.07170.1964-0.0070.57640.07170.23690.0019-0.00660.01880.0008-0.0280.06950.00290.00460.02610.07220.0074-0.00660.06740.00490.0795-39.083-0.4953-11.8719
91.2618-0.8298-0.42741.3353-0.52230.96360.02310.00330.0506-0.0420.03260.02230.0296-0.0327-0.05570.06580.0018-0.01340.0679-0.01420.108-43.856515.5175-9.1788
100.02850.0068-0.04540.30720.11860.12750.00380.00170.0086-0.0435-0.0120.0497-0.0181-0.00880.00820.08270.0048-0.00370.0677-0.0030.0823-31.078112.0804-17.523
110.16880.0055-0.0590.41140.00050.02090.00630.00660.0129-0.0609-0.00460.0445-0.00470.0002-0.00170.08380.0032-0.0080.0680.00030.0792-34.586921.0677-16.4571
120.06160.01110.04220.15860.01830.09830.00960.00970.0049-0.0149-0.0039-0.0035-0.00790.0007-0.00570.07350.000100.0662-0.00280.0834-24.12914.4286-10.2321
130.19260.14660.0090.5459-0.35990.31470.0058-0.00580.0265-0.0086-0.01730.02310.01160.02720.01150.07690.00320.00270.068-0.00340.0798-29.396422.8788-5.46
140.3697-0.1383-0.09280.1686-0.01680.04780.0076-0.04280.0353-0.0170.001-0.02160.00850.0078-0.00860.07340.0023-0.0030.0686-0.00380.0809-19.42232.9237-5.8853
150.29340.04240.03230.10090.05720.036-0.00570.01110.013-0.0150.0073-0.02710.0001-0.0017-0.00160.0773-0.00010.00260.06670.00150.0833-11.5550.41-15.9131
160.86430.13770.15390.0295-0.06041.73110.01420.02390.0526-0.0024-0.0157-0.00640.10430.08060.00150.05880.0132-0.0080.06410.01010.0963-2.6353-8.5279-20.7701
170.62920.00110.02830.0028-0.01620.0983-0.0036-0.0290.0049-0.00540.0019-0.0020.0253-0.00620.00170.07470.0024-0.00130.0654-0.00030.085-14.7936-11.6681-13.73
180.1495-0.1368-0.15770.17240.07530.6073-0.0036-0.0261-0.01910-0.0072-0.01930.0328-0.00090.01080.0598-0.00150.00220.07110.00360.088-7.6587-11.8236-7.7642
190.54560.00460.47460.02190.09350.77890.0003-0.0515-0.01140.0048-0.00240.00270.0227-0.04940.00210.0795-0.0012-0.00240.07570.00040.075-31.7497-7.3672-2.2357
201.37970.68330.74670.33890.36950.40470.0586-0.24350.07690.0236-0.11560.03410.0219-0.12790.0570.07-0.0239-0.00150.11290.00440.1079-43.8039-14.3679-8.4656
210.24010.16510.14320.18080.06610.10190.01480.04330.006-0.00530.00380.04410.01550.0316-0.01870.0808-0.0011-0.00360.0631-0.00730.0782-53.6692-6.64819.4629
220.2089-0.09940.0630.1702-0.10110.06090.0089-0.0026-0.01290.0099-0.01080.00020.00030.00230.00190.0783-0.0031-0.00270.06820.00040.0795-33.747-11.231417.7724
232.8258-0.94230.59740.3152-0.19850.1277-0.0114-0.0504-0.05990.01450.02630.0136-0.0048-0.0065-0.01490.1109-0.0011-0.01530.07180.0060.0944-33.6698-17.978325.4754
240.3285-0.09010.23670.1018-0.17280.32260.0203-0.0169-0.00720.0079-0.0130.0025-0.00870.0046-0.00740.0813-0.0082-0.00630.06980.00160.0806-24.9471-5.883524.8218
250.08130.3912-0.13891.8863-0.66960.23790.0089-0.0117-0.03140.0488-0.0681-0.1549-0.01870.0220.05920.0782-0.0103-0.01160.07080.00820.1006-18.44142.244820.8519
260.0068-0.01590.03020.0452-0.04950.40640.00510.02110.0108-0.016-0.0406-0.04560.02470.05350.03550.07770.0011-0.00220.08760.00540.0842-23.2601-4.054315.7449
271.35110.36270.14270.85380.03090.15970.02170.01840.0546-0.0092-0.05-0.07410.0372-0.00160.02830.06860.0008-0.00380.06190.00750.0945-23.745712.37768.9949
280.06020.0757-0.11080.5359-0.24540.23030.003-0.00460.00860.0639-0.0051-0.0534-0.01060.00480.00210.0851-0.0025-0.00350.06590.00190.0823-33.194413.348116.7285
290.9220.77620.02530.6625-0.01660.22910.0449-0.0417-0.02110.0599-0.0393-0.0251-0.02830.013-0.00560.0917-0.0031-0.01770.06480.00150.0948-23.921115.146317.8724
300.18120.06320.04490.3887-0.02510.0521-0.0045-0.00290.01320.03540.0018-0.0132-0.0037-0.0010.00280.0798-0.0017-0.00020.06440.00030.0784-37.804219.856113.3815
310.2389-0.0223-0.07340.50140.51630.57350.02850.01060.0188-0.0075-0.0361-0.0395-0.0155-0.03890.00760.0723-0.00130.00130.06340.00340.0857-36.381822.93665.3478
320.08370.19190.05830.44330.13790.0547-0.00450.00730.0029-0.02080.0141-0.00530.0038-0.0006-0.00960.07690.0004-0.00230.07040.00270.0779-44.35693.22546.0145
331.5226-0.2722-0.46250.0768-0.01190.47470.01910.0679-0.020.0024-0.02430.0132-0.02860.00330.00520.0811-0.0036-0.00010.0728-0.00310.0809-60.56070.22268.0737
340.4217-0.1719-0.08890.2544-0.14980.21030.0029-0.0009-0.0010.04820.00140.0219-0.03950.0081-0.00430.07710.00230.00160.06680.00110.082-49.40940.347717.3782
350.04910.05660.05520.1272-0.02240.1830.0068-0.0120.00740.0044-0.00940.00970.006-0.0150.00260.0734-0.00070.00580.0701-0.00170.0773-56.7598-0.45718.2893
361.4530.44950.39330.48090.9251.9954-0.0184-0.1240.06180.0219-0.1110.06580.0529-0.19240.12940.05150.0072-0.00960.06650.00760.0911-64.2778-8.162721.0361
370.38980.0232-0.02760.3367-0.05540.04210.00170.0044-0.0027-0.0103-0.00470.0067-0.0010.010.0030.07510.00010.00160.06660.0020.0819-51.1131-11.548113.8986
380.40670.3194-0.31970.4253-0.39960.928-0.010.0468-0.0122-0.01510.03960.05240.0707-0.0148-0.02960.06820.00180.00460.0538-0.00450.0871-58.1785-11.7497.962
391.0725-0.13150.4120.0199-0.02250.3914-0.00740.0109-0.06970.00590.00810.01490.02790.0241-0.00080.07930.0037-0.00190.0750.00090.0786-33.1297-7.7222.9627
4011.2922-3.0009-0.80250.80410.19580.10330.07490.64020.7422-0.0222-0.1477-0.21480.06160.10210.07280.08140.19550.06310.51050.18380.1241-22.5248-15.67487.8066
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 7
2X-RAY DIFFRACTION1A401 - 403
3X-RAY DIFFRACTION2A8 - 24
4X-RAY DIFFRACTION3A25 - 37
5X-RAY DIFFRACTION4A38 - 49
6X-RAY DIFFRACTION5A50 - 64
7X-RAY DIFFRACTION6A65 - 77
8X-RAY DIFFRACTION7A78 - 89
9X-RAY DIFFRACTION8A90 - 103
10X-RAY DIFFRACTION9A104 - 114
11X-RAY DIFFRACTION10A115 - 127
12X-RAY DIFFRACTION11A128 - 162
13X-RAY DIFFRACTION12A163 - 181
14X-RAY DIFFRACTION13A182 - 193
15X-RAY DIFFRACTION14A194 - 210
16X-RAY DIFFRACTION15A211 - 246
17X-RAY DIFFRACTION16A247 - 261
18X-RAY DIFFRACTION17A262 - 280
19X-RAY DIFFRACTION18A281 - 297
20X-RAY DIFFRACTION19A298 - 304
21X-RAY DIFFRACTION20A305 - 309
22X-RAY DIFFRACTION21B1 - 7
23X-RAY DIFFRACTION21B401 - 403
24X-RAY DIFFRACTION22B8 - 49
25X-RAY DIFFRACTION23B50 - 54
26X-RAY DIFFRACTION24B55 - 76
27X-RAY DIFFRACTION25B77 - 86
28X-RAY DIFFRACTION26B87 - 100
29X-RAY DIFFRACTION27B101 - 112
30X-RAY DIFFRACTION28B113 - 127
31X-RAY DIFFRACTION29B128 - 140
32X-RAY DIFFRACTION30B141 - 181
33X-RAY DIFFRACTION31B182 - 193
34X-RAY DIFFRACTION32B194 - 207
35X-RAY DIFFRACTION33B208 - 216
36X-RAY DIFFRACTION34B217 - 235
37X-RAY DIFFRACTION35B236 - 248
38X-RAY DIFFRACTION36B249 - 261
39X-RAY DIFFRACTION37B262 - 280
40X-RAY DIFFRACTION38B281 - 297
41X-RAY DIFFRACTION39B298 - 305
42X-RAY DIFFRACTION40B306 - 310

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