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- PDB-2for: Crystal Structure of the Shigella flexneri Farnesyl Pyrophosphate... -

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Basic information

Entry
Database: PDB / ID: 2for
TitleCrystal Structure of the Shigella flexneri Farnesyl Pyrophosphate Synthase Complex with an Isopentenyl Pyrophosphate
ComponentsGeranyltranstransferase
KeywordsTRANSFERASE / BISPHOSPHONATE / ISOPRENYL SYNTHASE / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


farnesyl diphosphate biosynthetic process / geranyltranstransferase activity / cytoplasm
Similarity search - Function
: / Polyprenyl synthases signature 2. / Polyprenyl synthases signature 1. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ISOPENTYL PYROPHOSPHATE / PHOSPHATE ION / : / Geranyltranstransferase
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsMinasov, G. / Brunzelle, J.S. / Shuvalova, L. / Collart, F.R. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of the Shigella flexneri Farnesyl Pyrophosphate Synthase Complex with an Isopentenyl Pyrophosphate
Authors: Minasov, G. / Brunzelle, J.S. / Shuvalova, L. / Collart, F.R. / Anderson, W.F.
History
DepositionJan 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 5, 2011Group: Structure summary
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

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Assembly

Deposited unit
A: Geranyltranstransferase
B: Geranyltranstransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,01011
Polymers69,8492
Non-polymers1,1619
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-80 kcal/mol
Surface area21260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.664, 75.664, 216.660
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
DetailsChains A and B represent the biological assembly, which is dimer

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Components

#1: Protein Geranyltranstransferase / E.C.2.5.1.10 / Farnesyl-diphosphate synthase / FPP synthase


Mass: 34924.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Strain: 301 / Gene: AAP15892 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3
References: GenBank: 24050587, UniProt: A0A0H2UXE9*PLUS, (2E,6E)-farnesyl diphosphate synthase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-IPR / ISOPENTYL PYROPHOSPHATE


Mass: 248.108 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H14O7P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.56 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES sodium salt, 0.4M Sodium phosphate, 0.4M Potassium phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 30, 2005 / Details: Mirrors
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→65.51 Å / Num. all: 45940 / Num. obs: 45940 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Rmerge(I) obs: 0.02 / Net I/σ(I): 57.66
Reflection shellResolution: 2→2.12 Å / Redundancy: 5.37 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 7.5 / Num. unique all: 6624 / % possible all: 87.8

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Processing

Software
NameVersionClassification
XDSdata scaling
XDSdata reduction
SHARPphasing
REFMAC5.2refinement
RefinementMethod to determine structure: SAD / Resolution: 2→65.51 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.943 / SU B: 11.046 / SU ML: 0.15 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Atomic isotropic B-factor refineme / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2329 2321 5 %RANDOM
Rwork0.18115 ---
all0.18369 ---
obs0.18369 43786 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 51.734 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å2-0.59 Å20 Å2
2---1.17 Å20 Å2
3---1.76 Å2
Refinement stepCycle: LAST / Resolution: 2→65.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4261 0 63 348 4672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224451
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.9946043
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.3915578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.0124.359195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.92815752
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2881534
X-RAY DIFFRACTIONr_chiral_restr0.1020.2686
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023354
X-RAY DIFFRACTIONr_nbd_refined0.2080.22474
X-RAY DIFFRACTIONr_nbtor_refined0.2970.23141
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2309
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.215
X-RAY DIFFRACTIONr_mcbond_it1.2151.52952
X-RAY DIFFRACTIONr_mcangle_it1.80624547
X-RAY DIFFRACTIONr_scbond_it3.05731655
X-RAY DIFFRACTIONr_scangle_it4.3774.51496
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 129 -
Rwork0.341 2741 -
obs--82.16 %
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)
114.4089-9.39451.11239.9592-1.15674.537-0.6493-1.54690.41151.06511.11550.9175-0.4457-0.592-0.46620.07490.16130.2210.19030.2721-0.0164-17.134331.51536.7409
211.0954-3.25251.25634.78590.0222.5508-0.2553-1.5135-0.01530.75570.56311.2154-0.3158-0.3852-0.3078-0.08330.06560.1638-0.06610.20620.0095-17.125233.070.7755
35.8665-0.1398-1.45136.7796-0.6672.9573-0.1375-0.6125-0.31380.34110.42411.56290.0466-0.1377-0.2866-0.19880.08470.0354-0.17060.20210.0058-16.743829.1749-2.1919
44.8626-0.0128-0.077210.254-0.45561.3689-0.1983-0.42450.77830.45740.44630.2636-0.40640.2158-0.248-0.13790.01920.0168-0.1281-0.0358-0.3038-3.217935.6315-2.3465
55.4535-1.4532-0.427811.0091-3.89696.50920.19170.2002-0.3503-0.4869-0.10831.3809-0.1692-0.1028-0.0834-0.1610.084-0.2444-0.23780.0388-0.0061-14.849227.2071-12.8471
62.6543.8136-4.352424.5023-23.230223.01560.36230.5461-0.3884-1.0136-0.09890.12290.3234-0.4315-0.26340.11760.1511-0.1889-0.17680.0394-0.1847-14.819243.0665-23.7526
73.8432-0.1787-1.71656.837-1.45184.9436-0.0247-0.0319-0.5759-0.848-0.0012.47530.4849-0.52080.0257-0.12340.0226-0.2955-0.16840.07950.6734-26.013927.7123-12.9572
811.53357.1417-2.467116.0908-1.54258.37120.05440.1981-1.4084-0.0431-0.15910.86060.4647-0.66070.1047-0.08830.0721-0.1579-0.1320.10190.0972-23.513741.9628-14.224
96.26562.3501-0.803111.9569-1.28962.4240.0806-0.1596-0.6875-0.42930.04721.3632-0.0954-0.2602-0.1278-0.00790.133-0.2083-0.14760.0611-0.0101-26.728547.691-16.3066
1012.88511.0982-1.523729.40241.47529.8086-0.1991-0.1689-0.07850.19030.50821.7365-1.103-0.6931-0.30910.04560.16360.0643-0.02830.24640.4036-30.374843.7573-5.8644
1122.0482-16.638-0.269717.9746-3.86953.06470.59440.6624-1.4887-2.1012-0.86520.59430.22340.15060.27080.51960.1383-0.27530.0547-0.1826-0.36124.38378.8292-24.2592
123.1686-1.7049-0.76919.2872-0.18371.05960.54280.4071-0.2542-1.1444-0.23550.22190.12520.1912-0.3073-0.01460.1134-0.1333-0.15880-0.40481.006217.7751-17.4208
135.5519-1.2445-0.88846.9889-0.25542.04710.40940.1907-0.3422-0.9164-0.21330.33250.00770.1711-0.1961-0.07240.0907-0.1388-0.20640.0083-0.4113-1.806921.7078-15.7265
1417.0835-0.56147.524910.61630.17457.0212-0.4712-0.54080.53270.78970.3498-0.4221-0.26350.45640.1214-0.1650.1117-0.0579-0.10510.0316-0.32251.88819.4116-0.2406
1530.81235.025217.92696.2319-2.05715.6925-0.2677-0.9345-0.20630.53750.02430.013-0.09860.1220.2434-0.1860.1023-0.0497-0.04150.015-0.37911.285213.99335.9602
169.4265-0.17773.53628.87473.54825.21250.0495-0.2795-1.5314-0.11560.07721.37720.2961-0.2464-0.1267-0.19220.0569-0.1289-0.20730.12980.0383-3.95445.3938-6.0984
1720.02685.52094.49269.19431.66112.48540.11440.0142-0.27820.32580.25770.80330.04190.4309-0.3721-0.14690.1267-0.0285-0.14810.0874-0.31586.94094.4677-3.3569
189.7184.22596.11913.4190.855714.5772-0.14310.69330.504-0.58170.4093-0.4687-0.30241.1835-0.2662-0.25670.0418-0.02780.2369-0.0104-0.279822.536111.9624-0.9551
1922.323113.62755.780818.35914.40726.5702-0.0863-0.7326-1.88470.69160.40670.06160.78890.3438-0.3204-0.00130.2371-0.0609-0.09380.1287-0.134810.3735-3.9558-2.8653
2029.64758.76082.144219.70533.21346.93210.0921-0.0352-0.6158-0.43310.1261-0.0232-0.03850.7767-0.2182-0.01280.1004-0.0857-0.12970.0153-0.414611.8134-0.7007-12.2032
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 3026 - 54
2X-RAY DIFFRACTION2AA31 - 5955 - 83
3X-RAY DIFFRACTION3AA60 - 8384 - 107
4X-RAY DIFFRACTION4AA84 - 125108 - 149
5X-RAY DIFFRACTION5AA126 - 168150 - 192
6X-RAY DIFFRACTION6AA169 - 179193 - 203
7X-RAY DIFFRACTION7AA180 - 208204 - 232
8X-RAY DIFFRACTION8AA209 - 224233 - 248
9X-RAY DIFFRACTION9AA225 - 281249 - 305
10X-RAY DIFFRACTION10AA282 - 299306 - 323
11X-RAY DIFFRACTION11BB1 - 2225 - 46
12X-RAY DIFFRACTION12BB23 - 9147 - 115
13X-RAY DIFFRACTION13BB92 - 138116 - 162
14X-RAY DIFFRACTION14BB139 - 168163 - 192
15X-RAY DIFFRACTION15BB169 - 179193 - 203
16X-RAY DIFFRACTION16BB180 - 205204 - 229
17X-RAY DIFFRACTION17BB206 - 221230 - 245
18X-RAY DIFFRACTION18BB222 - 259246 - 283
19X-RAY DIFFRACTION19BB260 - 281284 - 305
20X-RAY DIFFRACTION20BB282 - 298306 - 322

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