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- PDB-3glc: Crystal Structure of E. coli LsrF in complex with Ribose-5-phosphate -

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Basic information

Entry
Database: PDB / ID: 3glc
TitleCrystal Structure of E. coli LsrF in complex with Ribose-5-phosphate
ComponentsAldolase lsrF
KeywordsLYASE / TIM barrel / Schiff base
Function / homology
Function and homology information


3-hydroxy-5-phosphooxypentane-2,4-dione thiolase / fructose-bisphosphate aldolase activity / acyltransferase activity, transferring groups other than amino-acyl groups / cytoplasm
Similarity search - Function
3-hydroxy-5-phosphonooxypentane-2,4-dione thiolase / Aldolase FbaB-like, archaeal-type / DeoC/LacD family aldolase / DeoC/FbaB/LacD aldolase / DeoC/LacD family aldolase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
RIBOSE-5-PHOSPHATE / 3-hydroxy-5-phosphonooxypentane-2,4-dione thiolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsMiller, S.T. / Diaz, Z.C.
CitationJournal: Plos One / Year: 2009
Title: The crystal structure of the Escherichia coli autoinducer-2 processing protein LsrF.
Authors: Diaz, Z. / Xavier, K.B. / Miller, S.T.
History
DepositionMar 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Sep 6, 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 / 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

Downloads & links

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Assembly

Deposited unit
A: Aldolase lsrF
B: Aldolase lsrF
C: Aldolase lsrF
D: Aldolase lsrF
E: Aldolase lsrF
F: Aldolase lsrF
G: Aldolase lsrF
H: Aldolase lsrF
I: Aldolase lsrF
J: Aldolase lsrF
K: Aldolase lsrF
L: Aldolase lsrF
M: Aldolase lsrF
N: Aldolase lsrF
O: Aldolase lsrF
P: Aldolase lsrF
Q: Aldolase lsrF
R: Aldolase lsrF
S: Aldolase lsrF
T: Aldolase lsrF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)651,04540
Polymers646,44320
Non-polymers4,60220
Water6,017334
1
A: Aldolase lsrF
B: Aldolase lsrF
C: Aldolase lsrF
D: Aldolase lsrF
E: Aldolase lsrF
F: Aldolase lsrF
G: Aldolase lsrF
H: Aldolase lsrF
I: Aldolase lsrF
J: Aldolase lsrF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)325,52320
Polymers323,22110
Non-polymers2,30110
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area57840 Å2
ΔGint-241 kcal/mol
Surface area82660 Å2
MethodPISA
2
K: Aldolase lsrF
L: Aldolase lsrF
M: Aldolase lsrF
N: Aldolase lsrF
O: Aldolase lsrF
P: Aldolase lsrF
Q: Aldolase lsrF
R: Aldolase lsrF
S: Aldolase lsrF
T: Aldolase lsrF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)325,52320
Polymers323,22110
Non-polymers2,30110
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area57890 Å2
ΔGint-241 kcal/mol
Surface area82640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.352, 105.451, 173.415
Angle α, β, γ (deg.)89.51, 79.79, 90.34
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
131M
141N
151O
161P
171Q
181R
191S
201T

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 1 / Auth seq-ID: -99999 - 99999 / Label seq-ID: -99999 - 99999

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH
9II
10JJ
11KK
12LL
13MM
14NN
15OO
16PP
17QQ
18RR
19SS
20TT
Detailsbiological unit is a decamer. There are 2 biological units in the asymmetric unit (Chains ABCDEFGHIJ and chains KLMNOPQRST)

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Components

#1: Protein
Aldolase lsrF


Mass: 32322.145 Da / Num. of mol.: 20 / Fragment: Uncharacterized aldolase LsrF
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b1517, JW1510, lsrF, yneB / Plasmid: pGEX-4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P76143, Lyases; Carbon-carbon lyases; Aldehyde-lyases
#2: Sugar
ChemComp-R5P / RIBOSE-5-PHOSPHATE / Ribose 5-phosphate


Type: saccharideCarbohydrate / Mass: 230.110 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Formula: C5H11O8P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.3 Å3/Da / Density % sol: 46.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 4% PEG 400, 100 mM MgCl2, 2.3 M Ammonium Sulfate, pH 7.5, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 18, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→55.73 Å / Num. all: 327170 / Num. obs: 154484 / % possible obs: 81.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 45.3 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 7.5
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 1.8 / Num. unique all: 18764 / % possible all: 67.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.6data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
CBASSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3GKF

3gkf


Resolution: 2.5→55.73 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.911 / WRfactor Rfree: 0.235 / WRfactor Rwork: 0.208 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.837 / SU B: 10.846 / SU ML: 0.238 / SU Rfree: 0.405 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.405 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.235 6338 5 %RANDOM
Rwork0.205 ---
all0.206 127454 --
obs0.206 127454 67.42 %-
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: 108.88 Å2 / Biso mean: 35.975 Å2 / Biso min: 5.43 Å2
Baniso -1Baniso -2Baniso -3
1--2.42 Å2-1.47 Å2-0.47 Å2
2--1.71 Å22.8 Å2
3---0.81 Å2
Refinement stepCycle: LAST / Resolution: 2.5→55.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms42260 0 280 334 42874
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02243280
X-RAY DIFFRACTIONr_angle_refined_deg1.3581.96558560
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.57955480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.89623.8711860
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.675157380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.07515320
X-RAY DIFFRACTIONr_chiral_restr0.090.26580
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02132380
X-RAY DIFFRACTIONr_mcbond_it0.8371.527380
X-RAY DIFFRACTIONr_mcangle_it1.802244020
X-RAY DIFFRACTIONr_scbond_it3.239315900
X-RAY DIFFRACTIONr_scangle_it6.0044.514540
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2127 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
ATIGHT POSITIONAL0.050.05
BTIGHT POSITIONAL0.050.05
CTIGHT POSITIONAL0.050.05
DTIGHT POSITIONAL0.050.05
ETIGHT POSITIONAL0.050.05
FTIGHT POSITIONAL0.050.05
GTIGHT POSITIONAL0.050.05
HTIGHT POSITIONAL0.050.05
ITIGHT POSITIONAL0.060.05
JTIGHT POSITIONAL0.050.05
KTIGHT POSITIONAL0.050.05
LTIGHT POSITIONAL0.050.05
MTIGHT POSITIONAL0.050.05
NTIGHT POSITIONAL0.050.05
OTIGHT POSITIONAL0.050.05
PTIGHT POSITIONAL0.050.05
QTIGHT POSITIONAL0.050.05
RTIGHT POSITIONAL0.050.05
STIGHT POSITIONAL0.050.05
TTIGHT POSITIONAL0.050.05
ATIGHT THERMAL0.120.5
BTIGHT THERMAL0.110.5
CTIGHT THERMAL0.110.5
DTIGHT THERMAL0.120.5
ETIGHT THERMAL0.130.5
FTIGHT THERMAL0.120.5
GTIGHT THERMAL0.110.5
HTIGHT THERMAL0.130.5
ITIGHT THERMAL0.120.5
JTIGHT THERMAL0.120.5
KTIGHT THERMAL0.110.5
LTIGHT THERMAL0.110.5
MTIGHT THERMAL0.110.5
NTIGHT THERMAL0.120.5
OTIGHT THERMAL0.110.5
PTIGHT THERMAL0.120.5
QTIGHT THERMAL0.110.5
RTIGHT THERMAL0.110.5
STIGHT THERMAL0.120.5
TTIGHT THERMAL0.120.5
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 267 -
Rwork0.342 5138 -
all-5405 -
obs--38.56 %

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