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- PDB-2zgi: Crystal Structure of Putative 4-amino-4-deoxychorismate lyase -

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Basic information

Entry
Database: PDB / ID: 2zgi
TitleCrystal Structure of Putative 4-amino-4-deoxychorismate lyase
ComponentsPutative 4-amino-4-deoxychorismate lyase
KeywordsLYASE / TTHA0621 / PLP cofactor / pyridoxal enzyme / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, N-terminal / Branched-chain-amino-acid aminotransferase-like, C-terminal / Amino-transferase class IV / D-amino Acid Aminotransferase; Chain A, domain 1 / Alpha-Beta Barrel ...Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, N-terminal / Branched-chain-amino-acid aminotransferase-like, C-terminal / Amino-transferase class IV / D-amino Acid Aminotransferase; Chain A, domain 1 / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PYRIDOXAL-5'-PHOSPHATE / Putative 4-amino-4-deoxychorismate lyase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.93 Å
AuthorsPadmanabhan, B. / Bessho, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Structure of putative 4-amino-4-deoxychorismate lyase from Thermus thermophilus HB8.
Authors: Padmanabhan, B. / Bessho, Y. / Ebihara, A. / Antonyuk, S.V. / Ellis, M.J. / Strange, R.W. / Kuramitsu, S. / Watanabe, N. / Hasnain, S.S. / Yokoyama, S.
History
DepositionJan 22, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative 4-amino-4-deoxychorismate lyase
B: Putative 4-amino-4-deoxychorismate lyase
C: Putative 4-amino-4-deoxychorismate lyase
D: Putative 4-amino-4-deoxychorismate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,34217
Polymers109,3504
Non-polymers1,99213
Water23,7441318
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14650 Å2
ΔGint-121 kcal/mol
Surface area40250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.613, 133.585, 141.984
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Putative 4-amino-4-deoxychorismate lyase


Mass: 27337.592 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11-a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q5SKM2, Lyases

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Non-polymers , 5 types, 1331 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1318 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.8556.77
2
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.3M Li2SO4, 0.1M Na Hepes, pH 8.0, 25% Gly (cryo), VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11201
21202
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONSRS PX10.110.97892, 0.979, 0.92
ROTATING ANODERIGAKU FR-D22.29
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDFeb 16, 2007
RIGAKU RAXIS VII2IMAGE PLATEFeb 17, 2007
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal monochromater with sagittal focussingMADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.978921
20.9791
30.921
42.291
ReflectionResolution: 1.93→50 Å / Num. all: 94785 / Num. obs: 91735 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 13.1 % / Rmerge(I) obs: 0.063
Reflection shellResolution: 1.93→2 Å / Redundancy: 5 % / Rmerge(I) obs: 0.578 / Num. unique all: 6719 / % possible all: 72

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Processing

Software
NameVersionClassification
REFMAC5.4.0061refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
MOLREPphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.93→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.118 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Partial model, obtained from Cr-SAD solution, was used to trace full chain in Se-SAD solution in SOLVE, wARP/ARP.
RfactorNum. reflection% reflectionSelection details
Rfree0.24927 4573 5 %RANDOM
Rwork0.19327 ---
obs0.19618 86964 96.73 %-
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: 33.717 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å20 Å2
2--0.65 Å20 Å2
3----1.44 Å2
Refinement stepCycle: LAST / Resolution: 1.93→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7670 0 121 1318 9109
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0228050
X-RAY DIFFRACTIONr_angle_refined_deg1.5372.03410928
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3715996
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.52220.144347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.709151299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.78815117
X-RAY DIFFRACTIONr_chiral_restr0.0930.21181
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0226173
X-RAY DIFFRACTIONr_mcbond_it0.7981.54901
X-RAY DIFFRACTIONr_mcangle_it1.4427806
X-RAY DIFFRACTIONr_scbond_it2.35433149
X-RAY DIFFRACTIONr_scangle_it3.8314.53112
LS refinement shellResolution: 1.928→1.978 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 233 -
Rwork0.301 4329 -
obs--66.46 %

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