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- PDB-3tc1: Crystal Structure of Octaprenyl Pyrophosphate Synthase from Helic... -

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Basic information

Entry
Database: PDB / ID: 3tc1
TitleCrystal Structure of Octaprenyl Pyrophosphate Synthase from Helicobacter pylori
ComponentsOctaprenyl Pyrophosphate Synthase
KeywordsTRANSFERASE / all alpha-helices fold
Function / homology
Function and homology information


prenyltransferase activity / isoprenoid biosynthetic process
Similarity search - Function
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
Octaprenyl-diphosphate synthase (IspB)
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsZhang, J.Y. / Zhang, X.L. / Li, D.F. / Zou, Q.M. / Wang, D.C.
CitationJournal: To be Published
Title: Crystal Structure of Octaprenyl Pyrophosphate Synthase from Helicobacter pylori
Authors: Zhang, J.Y. / Zhang, X.L. / Li, D.F. / Zou, Q.M. / Wang, D.C.
History
DepositionAug 8, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2011Group: Advisory / Data collection
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_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_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: Octaprenyl Pyrophosphate Synthase
B: Octaprenyl Pyrophosphate Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3084
Polymers72,2602
Non-polymers492
Water9,674537
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-51 kcal/mol
Surface area26680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.330, 109.330, 103.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Octaprenyl Pyrophosphate Synthase


Mass: 36129.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: NCTC11637 / Gene: HP0240 / Plasmid: pET 22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O25023*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 537 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 15% PEG 3350, 100mM sodium acetate, 200mM MgCl2, pH 4.8, vapor diffusion, hanging drop, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-17A10.97901
SYNCHROTRONPhoton Factory BL-17A20.97888, 0.97926, 0.96403
Detector
TypeIDDetectorDate
RIGAKU RAXIS1IMAGE PLATEDec 18, 2008
RIGAKU RAXIS2IMAGE PLATEMay 20, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITESINGLE WAVELENGTHMx-ray1
2GRAPHITEMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979011
20.978881
30.979261
40.964031
ReflectionRedundancy: 14.2 % / Av σ(I) over netI: 5.2 / Number: 227777 / Rmerge(I) obs: 0.139 / Rsym value: 0.139 / D res high: 2.8 Å / D res low: 44.283 Å / Num. obs: 16095 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
8.8544.2899.210.0420.04211.6
6.268.8510010.0720.07213.2
5.116.2610010.1150.11513.7
4.435.1110010.0850.08514
3.964.4310010.090.0914.2
3.613.9610010.1170.11714.3
3.353.6110010.1590.15914.4
3.133.3510010.2160.21614.5
2.953.1310010.290.2914.5
2.82.9510010.3950.39514.6
ReflectionResolution: 2→54.665 Å / Num. all: 42895 / Num. obs: 42895 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 26.3 % / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 31.5
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2-2.1115.70.3780.36629617961080.0930.3780.3666.899.3
2.11-2.24240.2820.2762.613963458270.0570.2820.27612.9100
2.24-2.3929.30.2180.2143.316179655230.040.2180.21420.1100
2.39-2.5829.30.1650.1624.415022751270.030.1650.16225100
2.58-2.8329.20.1170.115613831747290.0220.1170.11533.6100
2.83-3.1629.10.0960.0946.612640843390.0180.0960.09444100
3.16-3.65290.0770.0767.611122638400.0140.0770.07654.1100
3.65-4.4728.60.0620.0619.49355632670.0110.0620.06160.6100
4.47-6.32280.0580.0579.27273326010.0110.0580.05759.2100
6.32-54.66525.20.0490.0488.93858715340.010.0490.04857.599.8

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Phasing

Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 42833
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
9.32-100450.736503
7.07-9.3234.40.776601
5.92-7.0739.80.735728
5.2-5.92370.778815
4.69-5.227.20.839930
4.3-4.6923.70.871007
4-4.3250.8571085
3.75-423.80.8551152
3.54-3.7525.60.8381213
3.37-3.5427.10.8131280
3.22-3.3728.60.7841331
3.08-3.2230.50.7611406
2.97-3.0830.30.731440
2.86-2.9735.30.6731500
2.77-2.8651.40.511564
2.68-2.7790.50.2941594
2.6-2.6891.70.2211642
2.53-2.688.80.2291695
2.46-2.5391.80.1881740
2.4-2.46910.1661798
2.35-2.489.30.1881807
2.29-2.3591.90.2621880
2.24-2.2990.20.221887
2.2-2.2490.20.2041965
2.15-2.291.30.1591967
2.11-2.15880.1642024
2.07-2.1189.60.2182057
2.04-2.0791.30.1062077
2-2.04900.0812145

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
DM6phasing
CNSrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→54.636 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2394 4314 10.1 %random
Rwork0.2006 ---
obs0.223 37172 99.9 %-
all-42832 --
Solvent computationBsol: 58.9148 Å2
Displacement parametersBiso max: 98.34 Å2 / Biso mean: 28.2343 Å2 / Biso min: 8.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.081 Å20 Å20 Å2
2--0.081 Å20 Å2
3----0.163 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.04 Å0.027 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2→54.636 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4757 0 2 537 5296
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.271
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param

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