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- PDB-3m0g: CRYSTAL STRUCTURE OF putative farnesyl diphosphate synthase from ... -

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Basic information

Entry
Database: PDB / ID: 3m0g
TitleCRYSTAL STRUCTURE OF putative farnesyl diphosphate synthase from Rhodobacter capsulatus
ComponentsFarnesyl diphosphate synthase
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NYSGXRC / Isoprene biosynthesis / PSI-2 / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


farnesyl diphosphate biosynthetic process / geranyltranstransferase activity / metal ion binding
Similarity search - Function
Polyprenyl synthases signature 1. / Polyprenyl synthases signature 2. / 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
Farnesyl diphosphate synthase
Similarity search - Component
Biological speciesRhodobacter capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 1.9 Å
AuthorsMalashkevich, V.N. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF putative farnesyl diphosphate synthase from Rhodobacter capsulatus
Authors: Malashkevich, V.N. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionMar 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_conn
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Farnesyl diphosphate synthase
B: Farnesyl diphosphate synthase


Theoretical massNumber of molelcules
Total (without water)62,4302
Polymers62,4302
Non-polymers00
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-39 kcal/mol
Surface area20720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.230, 90.680, 133.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Farnesyl diphosphate synthase


Mass: 31215.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / Gene: 8272412 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q9KWR7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS SATE THAT THIS PDB ENTRY HAS VERIFIED SEQUENCE FOR THE NYSGXRC-20032C TARGET WHICH HAS 12 ...AUTHORS SATE THAT THIS PDB ENTRY HAS VERIFIED SEQUENCE FOR THE NYSGXRC-20032C TARGET WHICH HAS 12 MISMATCHES RELATIVE TO THE PREVIOUSLY REPORTED SEQUENCE. THE SEQUENCE IS DIFFERENT FROM UNP ENTRY Q9KWR7

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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: 2.38 Å3/Da / Density % sol: 48.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG 1500, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionRedundancy: 3.4 % / Av σ(I) over netI: 19.28 / Number: 310949 / Rmerge(I) obs: 0.076 / Χ2: 1.12 / D res high: 1.9 Å / D res low: 50 Å / Num. obs: 90320 / % possible obs: 99.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.165098.110.0491.7763.6
4.095.1697.810.0511.8393.5
3.584.0998.310.0521.7553.3
3.253.5898.910.0571.5563.4
3.023.2599.210.0651.3943.5
2.843.0299.210.0741.2893.5
2.72.8499.210.0831.2333.5
2.582.79910.0931.1433.4
2.482.589910.1031.0843.4
2.392.4899.210.1111.0413.4
2.322.3999.110.130.9873.4
2.252.3299.610.1380.9343.4
2.192.2599.210.150.9243.4
2.142.1999.610.1760.8693.4
2.092.1499.310.1880.8193.4
2.052.0999.510.2190.783.5
2.012.0599.310.2610.7523.4
1.972.0199.710.3060.7323.5
1.931.9799.810.3360.6943.4
1.91.9399.710.4020.7263.5
ReflectionResolution: 1.9→50 Å / Num. obs: 90320 / % possible obs: 99.1 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.076 / Χ2: 1.117 / Net I/σ(I): 8.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.933.50.40244880.726199.7
1.93-1.973.40.33646360.694199.8
1.97-2.013.50.30644600.732199.7
2.01-2.053.40.26145590.752199.3
2.05-2.093.50.21944770.78199.5
2.09-2.143.40.18845860.819199.3
2.14-2.193.40.17644880.869199.6
2.19-2.253.40.1545630.924199.2
2.25-2.323.40.13844870.934199.6
2.32-2.393.40.1345290.987199.1
2.39-2.483.40.11145261.041199.2
2.48-2.583.40.10345281.084199
2.58-2.73.40.09344821.143199
2.7-2.843.50.08345261.233199.2
2.84-3.023.50.07444951.289199.2
3.02-3.253.50.06545801.394199.2
3.25-3.583.40.05744771.556198.9
3.58-4.093.30.05244891.755198.3
4.09-5.163.50.05144371.839197.8
5.16-503.60.04945071.776198.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.856 / WRfactor Rfree: 0.282 / WRfactor Rwork: 0.25 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.757 / SU B: 10.737 / SU ML: 0.146 / SU R Cruickshank DPI: 0.192 / SU Rfree: 0.173 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.192 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.294 2396 5 %RANDOM
Rwork0.261 ---
obs0.262 47501 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 72.21 Å2 / Biso mean: 13.812 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2--0.31 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3827 0 0 315 4142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223873
X-RAY DIFFRACTIONr_angle_refined_deg1.2321.9785262
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6315528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.77224.11146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.3315605
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0761527
X-RAY DIFFRACTIONr_chiral_restr0.0790.2637
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212893
X-RAY DIFFRACTIONr_mcbond_it0.7823.52632
X-RAY DIFFRACTIONr_mcangle_it2.931504119
X-RAY DIFFRACTIONr_scbond_it7.455501241
X-RAY DIFFRACTIONr_scangle_it0.8694.51143
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 174 -
Rwork0.292 3262 -
all-3436 -
obs--99.57 %
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)
10.6057-0.0612-0.67370.24990.2331.0642-0.02830.1586-0.07970.01850.0056-0.02240.0823-0.05410.02280.04440.0132-0.010.112-0.02290.072238.186240.792672.1328
20.7649-0.0453-0.20170.08440.26790.99470.09660.03830.05790.0055-0.00950.0037-0.0619-0.0602-0.08710.10650.01920.02070.0070.01620.092927.163257.998994.8326
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 286
2X-RAY DIFFRACTION2B2 - 287

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