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- PDB-2cfb: Glutamate-1-semialdehyde 2,1-Aminomutase from Thermosynechococcus... -

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Basic information

Entry
Database: PDB / ID: 2cfb
TitleGlutamate-1-semialdehyde 2,1-Aminomutase from Thermosynechococcus elongatus
ComponentsGLUTAMATE-1-SEMIALDEHYDE 2,1-AMINOMUTASE
KeywordsISOMERASE / TETRAPYRROLE BIOSYNTHESIS / PYRIDOXAL PHOSPHATE DEPENDENT / AMINOTRANSFERASE / PORPHYRIN BIOSYNTHESIS / CHLOROPHYLL BIOSYNTHESIS
Function / homology
Function and homology information


glutamate-1-semialdehyde 2,1-aminomutase / glutamate-1-semialdehyde 2,1-aminomutase activity / chlorophyll biosynthetic process / protoporphyrinogen IX biosynthetic process / transaminase activity / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Tetrapyrrole biosynthesis, glutamate-1-semialdehyde aminotransferase / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain ...Tetrapyrrole biosynthesis, glutamate-1-semialdehyde aminotransferase / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PLR / Glutamate-1-semialdehyde 2,1-aminomutase
Similarity search - Component
Biological speciesSYNECHOCOCCUS ELONGATUS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsSchulze, J.O. / Schubert, W.-D. / Moser, J. / Jahn, D. / Heinz, D.W.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Evolutionary Relationship between Initial Enzymes of Tetrapyrrole Biosynthesis
Authors: Schulze, J.O. / Schubert, W.-D. / Moser, J. / Jahn, D. / Heinz, D.W.
History
DepositionFeb 17, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
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 / _struct_conn.pdbx_leaving_atom_flag
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: PROVIDED BY DEPOSITIOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUTAMATE-1-SEMIALDEHYDE 2,1-AMINOMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7872
Polymers43,5541
Non-polymers2331
Water23413
1
A: GLUTAMATE-1-SEMIALDEHYDE 2,1-AMINOMUTASE
hetero molecules

A: GLUTAMATE-1-SEMIALDEHYDE 2,1-AMINOMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,5744
Polymers87,1082
Non-polymers4662
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)108.920, 108.920, 93.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein GLUTAMATE-1-SEMIALDEHYDE 2,1-AMINOMUTASE / GSA / GLUTAMATE-1-SEMIALDEHYDE AMINOTRANSFERASE / GSA-AT


Mass: 43553.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNECHOCOCCUS ELONGATUS (bacteria) / Strain: BP-1 / Plasmid: PETM30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: Q8DLK8, glutamate-1-semialdehyde 2,1-aminomutase
#2: Chemical ChemComp-PLR / (5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE / 4'-DEOXYPYRIDOXINE PHOSPHATE


Mass: 233.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H12NO5P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYTIC ACTIVITY: (S)-4-AMINO-5-OXOPENTANOATE = 5-AMINOLEVULINATE.

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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: 3.16 Å3/Da / Density % sol: 61 %
Crystal growpH: 6.5
Details: 100 MM PIPES PH 6.5, 200 MM MAGNESIUM SULFATE, 17% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU R-AXIS IV / Detector: IMAGE PLATE / Date: Feb 3, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 24944 / % possible obs: 99.5 % / Observed criterion σ(I): 3 / Redundancy: 4.2 % / Biso Wilson estimate: 48.8 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 10.42
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GSA

2gsa


Resolution: 2.85→19.96 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.923 / SU B: 26.669 / SU ML: 0.225 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.606 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 1-18, 132-159 AND 278-282 ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.22 678 5 %RANDOM
Rwork0.173 ---
obs0.176 12865 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.14 Å2
Baniso -1Baniso -2Baniso -3
1--3.75 Å20 Å20 Å2
2---3.75 Å20 Å2
3---7.5 Å2
Refinement stepCycle: LAST / Resolution: 2.85→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2717 0 15 13 2745
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222794
X-RAY DIFFRACTIONr_bond_other_d0.0010.022559
X-RAY DIFFRACTIONr_angle_refined_deg1.8261.9683790
X-RAY DIFFRACTIONr_angle_other_deg0.81835928
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0075357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.65623.793116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.81115436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8531514
X-RAY DIFFRACTIONr_chiral_restr0.120.2420
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023146
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02568
X-RAY DIFFRACTIONr_nbd_refined0.2460.2675
X-RAY DIFFRACTIONr_nbd_other0.2070.22662
X-RAY DIFFRACTIONr_nbtor_refined0.2090.21432
X-RAY DIFFRACTIONr_nbtor_other0.10.21723
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.276
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2110.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2640.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.72222187
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.65832826
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.37621170
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6663964
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.85→2.92 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.223 49
Rwork0.28 926
Refinement TLS params.Method: refined / Origin x: 29.132 Å / Origin y: 86.121 Å / Origin z: 39.495 Å
111213212223313233
T0.0974 Å2-0.0098 Å2-0.0558 Å2-0.2643 Å2-0.0825 Å2---0.0159 Å2
L2.8818 °2-0.0683 °2-0.7584 °2-1.6432 °2-0.0421 °2--0.9277 °2
S0.0822 Å °-0.4847 Å °0.2496 Å °0.2421 Å °-0.0461 Å °-0.0034 Å °-0.0592 Å °0.0828 Å °-0.0362 Å °

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