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- PDB-3lul: Crystal structure of Putative 4-amino-4-deoxychorismate lyase. (Y... -

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Basic information

Entry
Database: PDB / ID: 3lul
TitleCrystal structure of Putative 4-amino-4-deoxychorismate lyase. (YP_094631.1) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1 at 1.78 A resolution
Components4-amino-4-deoxychorismate lyase
KeywordsLYASE / Putative 4-amino-4-deoxychorismate lyase. / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Pyridoxal phosphate
Function / homology
Function and homology information


Aminotransferase, class IV, conserved site / Aminotransferases class-IV signature. / 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 ...Aminotransferase, class IV, conserved site / Aminotransferases class-IV signature. / 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
PHOSPHATE ION / 4-amino-4-deoxychorismate lyase
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.78 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative 4-amino-4-deoxychorismate lyase. (YP_094631.1) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1 at 1.78 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description
Category: pdbx_distant_solvent_atoms / software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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: 4-amino-4-deoxychorismate lyase
B: 4-amino-4-deoxychorismate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0377
Polymers62,6942
Non-polymers3435
Water9,584532
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-19 kcal/mol
Surface area22110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.008, 98.498, 64.599
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-276-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A2 - 268
2115B2 - 268

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Components

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


Mass: 31346.955 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg0595 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5ZXY5
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 532 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.16 Å3/Da / Density % sol: 42.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: 0.2000M (NH4)2HPO4, 20.0000% PEG-3350, No Buffer pH 7.9, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97951
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 6, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979511
ReflectionResolution: 1.78→45.592 Å / Num. obs: 52320 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.286 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 11.81
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.78-1.840.5382.4178214903199.6
1.84-1.920.3843.3205675616199.9
1.92-20.2644.9175714784199.8
2-2.110.1986.4200095471199.9
2.11-2.240.1448.6189165168199.7
2.24-2.410.11510.4187515137199.5
2.41-2.660.09112.6197565414199.4
2.66-3.040.06416.8188195172198.9
3.04-3.830.04423.5190245265198
3.83-45.5920.03528.3193265402196.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.78→45.592 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 0.23 / SU B: 5.271 / SU ML: 0.074 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.116
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. ETHYLENE GLYCOL (EDO) AND PHOSPHATE (PO4) MODELED WERE PRESENT IN CRYO/CRYSTALLIZATION BUFFER. 5. ELECTRON DENSITY REVEALS THAT RESIDUE LYS-140 IS COVALENTLY ATTACHED TO PYRIDOXAL-5'-PHOSPHATE (PLP) VIA A SCHIFF-BASE LINKAGE. THIS COVALENTLY MODIFIED RESIDUE HAS BEEN MODELED AS LYSINE-PYRIDOXAL-5'-PHOSPHATE (LLP).
RfactorNum. reflection% reflectionSelection details
Rfree0.201 2645 5.1 %RANDOM
Rwork0.16 ---
obs0.162 52290 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 70.74 Å2 / Biso mean: 16.954 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.15 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.78→45.592 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4327 0 21 532 4880
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224635
X-RAY DIFFRACTIONr_bond_other_d0.0020.023156
X-RAY DIFFRACTIONr_angle_refined_deg1.5341.9626330
X-RAY DIFFRACTIONr_angle_other_deg1.01837725
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5315597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.05624.13230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70415822
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8231535
X-RAY DIFFRACTIONr_chiral_restr0.0930.2718
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025176
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02949
X-RAY DIFFRACTIONr_mcbond_it1.74932774
X-RAY DIFFRACTIONr_mcbond_other0.70431116
X-RAY DIFFRACTIONr_mcangle_it2.96154538
X-RAY DIFFRACTIONr_scbond_it4.40781861
X-RAY DIFFRACTIONr_scangle_it6.809111758
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1521MEDIUM POSITIONAL0.230.5
1863LOOSE POSITIONAL0.385
1521MEDIUM THERMAL1.242
1863LOOSE THERMAL1.2310
LS refinement shellResolution: 1.78→1.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 186 -
Rwork0.252 3625 -
all-3811 -
obs--99.71 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.64260.14870.15930.69740.04280.4469-0.0008-0.026-0.05910.04190.01450.0378-0.0339-0.0474-0.01370.0060.00560.00490.00890.00670.014268.37257.634328.484
20.715-0.17870.22150.9315-0.17040.8801-0.09580.0806-0.0626-0.05360.07460.0465-0.065-0.10950.02120.0236-0.00760.00520.0524-0.00380.016555.143214.18260.7042
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 270
2X-RAY DIFFRACTION2B1 - 271

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