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- PDB-1gvf: Structure of tagatose-1,6-bisphosphate aldolase -

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Basic information

Entry
Database: PDB / ID: 1gvf
TitleStructure of tagatose-1,6-bisphosphate aldolase
ComponentsTAGATOSE-BISPHOSPHATE ALDOLASE AGAY
KeywordsLYASE / ZINC.
Function / homology
Function and homology information


tagatose-bisphosphate aldolase / tagatose-bisphosphate aldolase activity / D-tagatose 6-phosphate catabolic process / carbohydrate metabolic process / protein-containing complex / zinc ion binding / identical protein binding / cytosol
Similarity search - Function
D-tagatose-bisphosphate aldolase, class II, subunit KbaY/GatY / D-tagatose-bisphosphate aldolase, class II, subunit KbaY / Fructose-bisphosphate aldolase class-II signature 1. / Fructose-bisphosphate aldolase class-II signature 2. / Fructose-bisphosphate aldolase, class-II / Fructose-bisphosphate aldolase class-II / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PHOSPHOGLYCOLOHYDROXAMIC ACID / D-tagatose-1,6-bisphosphate aldolase subunit KbaY / D-tagatose-1,6-bisphosphate aldolase subunit KbaY
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 1.45 Å
AuthorsHall, D.R. / Hunter, W.N.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Structure of Tagatose-1,6-Bisphosphate Aldolase; Insight Into Chiral Discrimination, Mechanism and Specificity of Class II Aldolases
Authors: Hall, D.R. / Bond, C.S. / Leonard, G.A. / Watt, C.I. / Berry, A. / Hunter, W.N.
History
DepositionFeb 11, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2019Group: Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "BA" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "BA" IN EACH CHAIN ON SHEET RECORDS BELOW ARE ACTUALLY A 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TAGATOSE-BISPHOSPHATE ALDOLASE AGAY
B: TAGATOSE-BISPHOSPHATE ALDOLASE AGAY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,04922
Polymers62,6612
Non-polymers1,38820
Water11,854658
1
A: TAGATOSE-BISPHOSPHATE ALDOLASE AGAY
B: TAGATOSE-BISPHOSPHATE ALDOLASE AGAY
hetero molecules

A: TAGATOSE-BISPHOSPHATE ALDOLASE AGAY
B: TAGATOSE-BISPHOSPHATE ALDOLASE AGAY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,09844
Polymers125,3234
Non-polymers2,77640
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)72.650, 100.460, 206.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2053-

HOH

21A-2060-

HOH

31B-2047-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.02797, -0.99947, -0.01649), (-0.99951, 0.02819, -0.01366), (0.01412, 0.0161, -0.99977)
Vector: 51.48536, 49.7148, 87.68402)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein TAGATOSE-BISPHOSPHATE ALDOLASE AGAY / TAGATOSE-1 / 6-BISPHOSPHATE ALDOLASE


Mass: 31330.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P42908, UniProt: P0AB74*PLUS, tagatose-bisphosphate aldolase

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Non-polymers , 5 types, 678 molecules

#2: Chemical ChemComp-PGH / PHOSPHOGLYCOLOHYDROXAMIC ACID


Mass: 171.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6NO6P
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 658 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHE ASYMMETRIC UNIT CONTAINS A DIMER WHICH BY MEANS OF A CRYSTALLOGRAPHIC TWO-FOLD SYMMETRY ...THE ASYMMETRIC UNIT CONTAINS A DIMER WHICH BY MEANS OF A CRYSTALLOGRAPHIC TWO-FOLD SYMMETRY OPERATOR FORMS THE FUNCTIONAL TETRAMERIC ENZYME

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.7 %
Description: WAVELENGTHS QUOTED ARE FOR MAD PEAK, MAD INFLECTION POINT, MAD REMOTE 1, MAD REMOTE2, INHOUSE REFINEMENT, ID14-EH2 HIGH RES REFINEMENT DATA SETS RESPECTIVELY EXPERIMENTAL STATISTICS ...Description: WAVELENGTHS QUOTED ARE FOR MAD PEAK, MAD INFLECTION POINT, MAD REMOTE 1, MAD REMOTE2, INHOUSE REFINEMENT, ID14-EH2 HIGH RES REFINEMENT DATA SETS RESPECTIVELY EXPERIMENTAL STATISTICS QUOTED FOR COMBINED INHOUSE AND HIGH RES DATA SET USED FOR REFINEMENT
Crystal growpH: 6.4 / Details: pH 6.40
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16.5 mg/mlenzyme1drop
250 mMTris-HCl1droppH7.5
320 mMPGH1drop
47-12 %(v/v)ethylene glycol1reservoir
510 mM1reservoirZnCl2
642 mMsodium cacodylate1reservoirpH6.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.282,1.283,1.127,1.030, 1.5418,0.933
DetectorType: MAR, RAXIS / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.2821
21.2831
31.1271
41.031
51.54181
60.9331
ReflectionResolution: 1.45→29.8 Å / Num. obs: 1086028 / % possible obs: 98.4 % / Redundancy: 3 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 15
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 3 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 1.5 / % possible all: 97.9
Reflection
*PLUS
Num. obs: 131455 / Num. measured all: 1086028

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Processing

Software
NameClassification
DENZOdata reduction
MOSFLMdata reduction
SCALEPACKdata scaling
SCALAdata scaling
RSPSphasing
MLPHAREphasing
SHELXL-97refinement
RefinementMethod to determine structure: DIRECT METHODS / Resolution: 1.45→10 Å / Num. parameters: 47082 / Num. restraintsaints: 56585 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ARP/WARP WITH REFMAC USED FIRST FOLLOWED BY CNS THE FOLLOWING RESIDUES HAVE MISSING ATOMS DUE TO DISORDER: SER A 151 LYS A 185 LYS A 188 ARG A 257 SER A 285 GLU B 150 SER B 151 LYS B 185 LYS B 188 GLU B 216
RfactorNum. reflection% reflectionSelection details
Rfree0.1733 6592 5.3 %RANDOM
all0.1268 124490 --
obs0.131 -93.4 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 15 / Occupancy sum hydrogen: 4167 / Occupancy sum non hydrogen: 4926.25
Refinement stepCycle: LAST / Resolution: 1.45→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4189 0 80 658 4927
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.018
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0253
X-RAY DIFFRACTIONs_zero_chiral_vol0.047
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.062
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.097
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.055
X-RAY DIFFRACTIONs_approx_iso_adps0.086
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / Rfactor all: 0.13 / Rfactor obs: 0.17 / Rfactor Rfree: 0.13
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_plane_restr0.025
X-RAY DIFFRACTIONs_chiral_restr0.062

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