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- PDB-3fdb: Crystal structure of a putative plp-dependent beta-cystathionase ... -

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Basic information

Entry
Database: PDB / ID: 3fdb
TitleCrystal structure of a putative plp-dependent beta-cystathionase (aecd, dip1736) from corynebacterium diphtheriae at 1.99 A resolution
Componentsputative PLP-dependent beta-cystathionase
KeywordsTRANSFERASE / Plp-dependent transferase-like fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Hydrolases / biosynthetic process / pyridoxal phosphate binding / lyase activity / hydrolase activity
Similarity search - Function
Aminotransferase, class I/classII / Aminotransferase class I and II / 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 ...Aminotransferase, class I/classII / Aminotransferase class I and II / 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
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.99 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative PLP-dependent beta-cystathionase (NP_940074.1) from CORYNEBACTERIUM DIPHTHERIAE at 1.99 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: 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 / _struct_conn.pdbx_leaving_atom_flag
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

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Assembly

Deposited unit
A: putative PLP-dependent beta-cystathionase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,13416
Polymers42,3761
Non-polymers75915
Water7,764431
1
A: putative PLP-dependent beta-cystathionase
hetero molecules

A: putative PLP-dependent beta-cystathionase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,26932
Polymers84,7512
Non-polymers1,51830
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area9020 Å2
ΔGint-97 kcal/mol
Surface area27080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.180, 69.180, 215.460
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-378-

CL

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Components

#1: Protein putative PLP-dependent beta-cystathionase / Beta C-S lyase


Mass: 42375.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Gene: aecD, DIP1736, NP_940074.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q6NFZ9, Hydrolases
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 431 / 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: 3.51 Å3/Da / Density % sol: 64.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2000M MgCl2, 10.0000% PEG-3000, 0.1M Cacodylate pH 6.5, 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: 0.91837,0.97934,0.97922
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 3, 2008 / 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
20.979341
30.979221
ReflectionResolution: 1.99→29.961 Å / Num. obs: 47285 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.512 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 10.77
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.91-1.980.731.5259549056198.5
1.98-2.060.4962.1255478870198.5
2.06-2.150.3572.9244078463198.4
2.15-2.260.2514.1248838628199
2.26-2.410.1695.8272379419199.2
2.41-2.590.1277.6248978581199.3
2.59-2.850.08511.2259478939199.5
2.85-3.260.05416.9258528902199.5
3.26-4.10.03525257778906199.3
4.1-29.9610.02729.9263259039199.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.99→29.961 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 5.231 / SU ML: 0.077 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.106
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.SODIUM ION, ETHYLENE GLYCOL MOLECULES AND CHLORIDE IONS FROM CRYSTALLIZATION AND CRYOPROTECTANT ARE MODELED INTO THISSTRUCTURE, RESPECTIVELY. 5.ONE PLP MOLECULE FROM PROTEIN EXPRESSION ARE MODELED IN THIS STRUCTURE WITH CLEAR ELECTRON DENSITY SUPPORT.
RfactorNum. reflection% reflectionSelection details
Rfree0.175 2140 5.1 %RANDOM
Rwork0.147 ---
obs0.149 41858 99.43 %-
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 max: 102.45 Å2 / Biso mean: 43.667 Å2 / Biso min: 17.82 Å2
Baniso -1Baniso -2Baniso -3
1-2.28 Å21.14 Å20 Å2
2--2.28 Å20 Å2
3----3.42 Å2
Refinement stepCycle: LAST / Resolution: 1.99→29.961 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2950 0 42 431 3423
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223138
X-RAY DIFFRACTIONr_bond_other_d0.0010.022087
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.9484277
X-RAY DIFFRACTIONr_angle_other_deg0.96735069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.655392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.31523.931145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.18515464
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8911517
X-RAY DIFFRACTIONr_chiral_restr0.0950.2458
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023565
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02658
X-RAY DIFFRACTIONr_nbd_refined0.2130.3672
X-RAY DIFFRACTIONr_nbd_other0.1960.32188
X-RAY DIFFRACTIONr_nbtor_refined0.1840.51581
X-RAY DIFFRACTIONr_nbtor_other0.0910.51435
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.5526
X-RAY DIFFRACTIONr_metal_ion_refined0.1980.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.324
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2720.374
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2480.537
X-RAY DIFFRACTIONr_mcbond_it1.57931931
X-RAY DIFFRACTIONr_mcbond_other0.483771
X-RAY DIFFRACTIONr_mcangle_it2.52553120
X-RAY DIFFRACTIONr_scbond_it5.01581260
X-RAY DIFFRACTIONr_scangle_it7.027111157
LS refinement shellResolution: 1.99→2.042 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 129 -
Rwork0.221 2899 -
all-3028 -
obs--98.66 %
Refinement TLS params.Method: refined / Origin x: -12.2433 Å / Origin y: 33.2793 Å / Origin z: 18.824 Å
111213212223313233
T-0.0893 Å2-0.0499 Å20.0319 Å2--0.0802 Å2-0.0141 Å2---0.0647 Å2
L0.4085 °20.1468 °2-0.076 °2-0.6188 °20.0426 °2--1.1808 °2
S-0.0128 Å °0.0069 Å °-0.0026 Å °-0.0614 Å °0.0366 Å °-0.0029 Å °-0.0633 Å °0.1023 Å °-0.0239 Å °

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