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- PDB-1gt7: L-rhamnulose-1-phosphate aldolase from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 1gt7
TitleL-rhamnulose-1-phosphate aldolase from Escherichia coli
ComponentsRHAMNULOSE-1-PHOSPHATE ALDOLASE
KeywordsLYASE / ALDOLASE (LYASE) / CLASS II / ZINC ENZYME / BACTERIAL L- RHAMNOSE METABOLISM / CLEAVAGE OF L-RHAMNULOSE-1-PHOSPHATE TO DIHYDROXYACETONEPHOSPHATE AND L-LACTALDEHYDE
Function / homology
Function and homology information


rhamnulose-1-phosphate aldolase / rhamnulose-1-phosphate aldolase activity / rhamnose catabolic process / pentose catabolic process / aldehyde-lyase activity / metal ion binding / identical protein binding / cytosol
Similarity search - Function
Rhamnulose-1-phosphate aldolase / : / L-fuculose-1-phosphate Aldolase / Class II aldolase/adducin N-terminal domain / Class II aldolase/adducin N-terminal / Class II Aldolase and Adducin N-terminal domain / Class II Aldolase and Adducin N-terminal domain / Class II aldolase/adducin N-terminal domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOGLYCOLOHYDROXAMIC ACID / Rhamnulose-1-phosphate aldolase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 2.7 Å
AuthorsKroemer, M. / Schulz, G.E.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: The Structure of L-Rhamnulose-1-Phosphate Aldolase (Class II) Solved by Low-Resolution Sir Phasing and 20-Fold Ncs Averaging
Authors: Kroemer, M. / Schulz, G.E.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: Structures of L-Fuculose-1-Phosphate Aldolase Mutants Outlining Motions During Catalysis
Authors: Joerger, A.C. / Mueller-Dieckmann, C. / Schulz, G.E.
#2: Journal: J.Bacteriol. / Year: 1993
Title: Sequencing and Characterization of a Gene Cluster Encoding the Enzymes for L-Rhamnose Metabolism in Escherichia Coli
Authors: Moralejo, P. / Egan, S.M. / Hidalgo, E. / Aguilar, J.
History
DepositionJan 14, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 3, 2002Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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.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_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_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_conn.ptnr2_label_seq_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: RHAMNULOSE-1-PHOSPHATE ALDOLASE
B: RHAMNULOSE-1-PHOSPHATE ALDOLASE
C: RHAMNULOSE-1-PHOSPHATE ALDOLASE
D: RHAMNULOSE-1-PHOSPHATE ALDOLASE
E: RHAMNULOSE-1-PHOSPHATE ALDOLASE
F: RHAMNULOSE-1-PHOSPHATE ALDOLASE
G: RHAMNULOSE-1-PHOSPHATE ALDOLASE
H: RHAMNULOSE-1-PHOSPHATE ALDOLASE
I: RHAMNULOSE-1-PHOSPHATE ALDOLASE
J: RHAMNULOSE-1-PHOSPHATE ALDOLASE
K: RHAMNULOSE-1-PHOSPHATE ALDOLASE
L: RHAMNULOSE-1-PHOSPHATE ALDOLASE
M: RHAMNULOSE-1-PHOSPHATE ALDOLASE
N: RHAMNULOSE-1-PHOSPHATE ALDOLASE
O: RHAMNULOSE-1-PHOSPHATE ALDOLASE
P: RHAMNULOSE-1-PHOSPHATE ALDOLASE
Q: RHAMNULOSE-1-PHOSPHATE ALDOLASE
R: RHAMNULOSE-1-PHOSPHATE ALDOLASE
S: RHAMNULOSE-1-PHOSPHATE ALDOLASE
T: RHAMNULOSE-1-PHOSPHATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)608,21760
Polymers603,48820
Non-polymers4,72940
Water62,6923480
1
A: RHAMNULOSE-1-PHOSPHATE ALDOLASE
B: RHAMNULOSE-1-PHOSPHATE ALDOLASE
C: RHAMNULOSE-1-PHOSPHATE ALDOLASE
D: RHAMNULOSE-1-PHOSPHATE ALDOLASE
hetero molecules

A: RHAMNULOSE-1-PHOSPHATE ALDOLASE
B: RHAMNULOSE-1-PHOSPHATE ALDOLASE
C: RHAMNULOSE-1-PHOSPHATE ALDOLASE
D: RHAMNULOSE-1-PHOSPHATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,28724
Polymers241,3958
Non-polymers1,89216
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
MethodPQS
2
E: RHAMNULOSE-1-PHOSPHATE ALDOLASE
F: RHAMNULOSE-1-PHOSPHATE ALDOLASE
G: RHAMNULOSE-1-PHOSPHATE ALDOLASE
H: RHAMNULOSE-1-PHOSPHATE ALDOLASE
hetero molecules

Q: RHAMNULOSE-1-PHOSPHATE ALDOLASE
R: RHAMNULOSE-1-PHOSPHATE ALDOLASE
S: RHAMNULOSE-1-PHOSPHATE ALDOLASE
T: RHAMNULOSE-1-PHOSPHATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,28724
Polymers241,3958
Non-polymers1,89216
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
MethodPQS
3
I: RHAMNULOSE-1-PHOSPHATE ALDOLASE
J: RHAMNULOSE-1-PHOSPHATE ALDOLASE
K: RHAMNULOSE-1-PHOSPHATE ALDOLASE
L: RHAMNULOSE-1-PHOSPHATE ALDOLASE
hetero molecules

M: RHAMNULOSE-1-PHOSPHATE ALDOLASE
N: RHAMNULOSE-1-PHOSPHATE ALDOLASE
O: RHAMNULOSE-1-PHOSPHATE ALDOLASE
P: RHAMNULOSE-1-PHOSPHATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,28724
Polymers241,3958
Non-polymers1,89216
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
MethodPQS
4
M: RHAMNULOSE-1-PHOSPHATE ALDOLASE
N: RHAMNULOSE-1-PHOSPHATE ALDOLASE
O: RHAMNULOSE-1-PHOSPHATE ALDOLASE
P: RHAMNULOSE-1-PHOSPHATE ALDOLASE
hetero molecules

I: RHAMNULOSE-1-PHOSPHATE ALDOLASE
J: RHAMNULOSE-1-PHOSPHATE ALDOLASE
K: RHAMNULOSE-1-PHOSPHATE ALDOLASE
L: RHAMNULOSE-1-PHOSPHATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,28724
Polymers241,3958
Non-polymers1,89216
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
MethodPQS
5
Q: RHAMNULOSE-1-PHOSPHATE ALDOLASE
R: RHAMNULOSE-1-PHOSPHATE ALDOLASE
S: RHAMNULOSE-1-PHOSPHATE ALDOLASE
T: RHAMNULOSE-1-PHOSPHATE ALDOLASE
hetero molecules

E: RHAMNULOSE-1-PHOSPHATE ALDOLASE
F: RHAMNULOSE-1-PHOSPHATE ALDOLASE
G: RHAMNULOSE-1-PHOSPHATE ALDOLASE
H: RHAMNULOSE-1-PHOSPHATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,28724
Polymers241,3958
Non-polymers1,89216
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
MethodPQS
Unit cell
Length a, b, c (Å)225.760, 225.760, 285.645
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.00728, 0.99923, 0.03847), (-0.98919, 0.00156, 0.1466), (0.14643, -0.03912, 0.98845)-73.2682, 4.95113, 6.55085
3given(-0.98225, 0.00894, 0.18735), (0.0112, -0.99429, 0.10614), (0.18723, 0.10635, 0.97654)-68.8147, 78.41696, 2.31355
4given(0.0104, -0.98842, 0.15139), (0.99908, 0.00399, -0.0426), (0.0415, 0.15169, 0.98756)4.17451, 73.59242, -4.48996
5given(-0.79023, -0.00815, 0.61276), (-0.00959, -0.99962, -0.02567), (0.61274, -0.02616, 0.78985)-84.36285, 163.48059, 31.17487
6given(0.0892, -0.813, 0.5754), (0.98563, -0.01116, -0.16857), (0.14347, 0.58216, 0.80031)-22.74884, 158.88541, -8.77978
7given(0.8903, 0.06604, 0.45056), (-0.00557, 0.99093, -0.13423), (-0.45534, 0.117, 0.8826)-29.31088, 85.82259, -11.27663
8given(0.01073, 0.87616, 0.4819), (-0.99991, 0.00581, 0.01171), (0.00746, -0.48198, 0.87615)-90.84985, 90.04077, 27.72077
9given(0.02672, -0.99957, 0.01209), (0.87699, 0.01763, -0.48018), (0.47976, 0.02343, 0.87709)90.64722, 91.28036, 17.28046
10given(0.9912, 0.02425, -0.13012), (-0.07949, 0.89514, -0.43864), (0.10584, 0.44513, 0.88919)83.6416, 24.09704, -12.13899
11given(-0.03464, 0.99522, -0.09129), (-0.94978, -0.06121, -0.30686), (-0.31098, 0.07607, 0.94737)10.59214, 31.6264, -12.03255
12given(-0.99805, -0.02752, 0.05603), (0.00695, -0.94102, -0.33827), (0.06203, -0.33722, 0.93938)17.23679, 98.21745, 16.69319
13given(0.89573, -0.01697, -0.44426), (0.07096, 0.99192, 0.10519), (0.43889, -0.12575, 0.8897)21.52765, -80.72582, 32.93923
14given(-0.03543, 0.91259, -0.40733), (-0.96548, 0.07399, 0.24975), (0.25806, 0.40212, 0.87847)-46.84107, -80.43912, 5.97286
15given(-0.96291, -0.0195, -0.26912), (-0.04254, -0.97395, 0.22276), (-0.26646, 0.22594, 0.93699)-42.46217, -7.80133, -5.21833
16given(-0.02643, -0.95233, -0.30393), (0.99582, -0.05167, 0.0753), (-0.08741, -0.30067, 0.94972)26.14126, -8.07467, 21.53089
17given(0.08642, 0.98728, 0.13346), (-0.80821, -0.00885, 0.58882), (0.58251, -0.15875, 0.79717)-152.5056, -12.27797, 46.81649
18given(-0.95648, 0.08246, 0.27992), (0.08855, -0.83199, 0.54767), (0.27805, 0.54863, 0.78848)-153.08629, 50.91986, 8.55401
19given(-0.04838, -0.96556, 0.25563), (0.90263, 0.06732, 0.42512), (-0.42769, 0.2513, 0.86829)-81.05338, 43.67205, -4.00046
20given(0.99238, -0.06161, 0.10672), (0.00583, 0.88855, 0.45874), (-0.12309, -0.45462, 0.88214)-80.37141, -18.95387, 33.82193
DetailsTHE PROTEIN IS ACTIVE AS TETRAMER

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Components

#1: Protein
RHAMNULOSE-1-PHOSPHATE ALDOLASE


Mass: 30174.404 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PKK223-3 (GEN RHAD) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM105
References: UniProt: P32169, rhamnulose-1-phosphate aldolase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-PGH / PHOSPHOGLYCOLOHYDROXAMIC ACID


Mass: 171.046 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3480 / 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: 3.5 Å3/Da / Density % sol: 65 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.6
Details: HANGING DROP CONTAINED 5 MG/ML PROTEIN, 5 MM PGH, 0.9 M SODIUM FORMATE, 5 MM MERCAPTOETHANOL, 0.5 MM ZNCL2 AND 0.1 M SODIUM ACETATE (PH 4.6). RESERVOIR CONTAINED 1.8 M SODIUM FORMATE, 5 MM ...Details: HANGING DROP CONTAINED 5 MG/ML PROTEIN, 5 MM PGH, 0.9 M SODIUM FORMATE, 5 MM MERCAPTOETHANOL, 0.5 MM ZNCL2 AND 0.1 M SODIUM ACETATE (PH 4.6). RESERVOIR CONTAINED 1.8 M SODIUM FORMATE, 5 MM MERCAPTOETHANOL AND 0.1 M SODIUM ACETATE (PH 4.6)
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
15 mg/mlprotein1drop
25 mMphosphoglycolohydroxamate1drop
30.9 Msodium formate1drop
45 mMbeta-mercaptoethanol1drop
50.5 mM1dropZnCl2
60.1 Msodium acetate1droppH4.6
71.8 Msodium formate1reservoir
85 mMbeta-mercaptoethanol1reservoir
90.1 Msodium acetate1reservoirpH4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.907
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.907 Å / Relative weight: 1
ReflectionResolution: 2.7→45 Å / Num. obs: 207606 / % possible obs: 90.7 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 7.8
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 2.1 / % possible all: 89.8
Reflection
*PLUS
Lowest resolution: 45 Å / % possible obs: 91 % / Num. measured all: 611276
Reflection shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.8 Å / % possible obs: 90 % / Rmerge(I) obs: 0.37

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Processing

Software
NameClassification
DMmodel building
SCALAdata scaling
SCALEITphasing
MLPHAREphasing
GETAXphasing
DMphasing
REFMACrefinement
RefinementMethod to determine structure: SIR / Resolution: 2.7→44 Å / SU B: 11.6 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R Free: 0.31
Details: THE TWENTYFOLD NON-CRYSTALLOGRAPHIC SYMMETRY WAS ALWAYS TIGHTLY RESTRAINED ARRANGING THE TWENTY PROTEIN CHAINS IN ONE NCS GROUP, AND THE TWENTY ZN IONS, PGH MOLECULES AND WATER MOLECULE ...Details: THE TWENTYFOLD NON-CRYSTALLOGRAPHIC SYMMETRY WAS ALWAYS TIGHTLY RESTRAINED ARRANGING THE TWENTY PROTEIN CHAINS IN ONE NCS GROUP, AND THE TWENTY ZN IONS, PGH MOLECULES AND WATER MOLECULE CHAINS AS A SECOND NCS GROUP. THE GEOMETRY AND VDW DISTANCES OF SOME SURFACE RESIDUES WERE THEREFORE DISTURBED DUE TO CLASHES IN CRYSTAL CONTACTS THAT DO NOT FOLLOW THE OVERALL NON-CRYSTALLOGRAPHIC SYMMETRY.
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1036 0.5 %RANDOM
Rwork0.233 ---
obs-207386 90.3 %-
Refinement stepCycle: LAST / Resolution: 2.7→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms42480 0 220 3480 46180
Refinement
*PLUS
Lowest resolution: 44 Å / Rfactor obs: 0.233
Solvent computation
*PLUS
Displacement parameters
*PLUS

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