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- PDB-3i16: Crystal structure of carbon-sulfur lyase involved in aluminum res... -

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Basic information

Entry
Database: PDB / ID: 3i16
TitleCrystal structure of carbon-sulfur lyase involved in aluminum resistance (YP_878183.1) from Clostridium novyi NT at 2.00 A resolution
ComponentsAluminum resistance protein
KeywordsLYASE / YP_878183.1 / carbon-sulfur lyase involved in aluminum resistance / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Putative methionine gamma-lyase / Methionine gamma-lyase / Methioning gamme-lyase, C-terminal domain / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / L(+)-TARTARIC ACID / Aluminum resistance protein
Similarity search - Component
Biological speciesClostridium novyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of carbon-sulfur lyase involved in aluminum resistance (YP_878183.1) from Clostridium novyi NT at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / 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

Downloads & links

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Assembly

Deposited unit
A: Aluminum resistance protein
B: Aluminum resistance protein
C: Aluminum resistance protein
D: Aluminum resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,07428
Polymers191,1354
Non-polymers1,93924
Water18,0871004
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26100 Å2
ΔGint-40 kcal/mol
Surface area50500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.645, 108.999, 207.556
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A0 - 60
2114B0 - 60
3114C0 - 60
4114D0 - 60
1216A61 - 70
2216B61 - 70
3216C61 - 70
4216D61 - 70
1314A71 - 184
2314B71 - 184
3314C71 - 184
4314D71 - 184
1416A185 - 190
2416B185 - 190
3416C185 - 190
4416D185 - 190
1514A191 - 335
2514B191 - 335
3514C191 - 335
4514D191 - 335
1616A336 - 350
2616B336 - 350
3616C336 - 350
4616D336 - 350
1714A351 - 360
2714B351 - 360
3714C351 - 360
4714D351 - 360
1816A361 - 380
2816B361 - 380
3816C361 - 380
4816D361 - 380
1914A381 - 395
2914B381 - 395
3914C381 - 395
4914D381 - 395
11016A396 - 406
21016B396 - 406
31016C396 - 406
41016D396 - 406
11114A407 - 423
21114B407 - 423
31114C407 - 423
41114D407 - 423
11216A424 - 426
21216B424 - 426
31216C424 - 426
41216D424 - 426
DetailsSTATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A TETRAMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein
Aluminum resistance protein / carbon-sulfur lyase


Mass: 47783.688 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium novyi (bacteria) / Strain: NT / Gene: NT01CX_2110, YP_878183.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A0Q0N1
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1004 / 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: 2.33 Å3/Da / Density % sol: 47.15 %
Crystal growTemperature: 293 K
Details: 20.9000% polyethylene glycol 3350, 0.2360M di-ammonium tartrate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97959,0.97944
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 19, 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
10.911621
20.979591
30.979441
ReflectionResolution: 2→29.775 Å / Num. obs: 120764 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 27.26 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 9.16
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.676 / Mean I/σ(I) obs: 1.1 / % possible all: 100

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SCALAdata scaling
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2→29.77 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 8.393 / SU ML: 0.104 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.149
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS RIDING POSITIONS. 2). ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE ...Details: 1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS RIDING POSITIONS. 2). ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THESE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4). ETHYLENE GLYCOL USED AS A CRYOGEN WAS MODELED INTO THE STRUCTURE. 5). IN THE STRUCTURE OF THIS PROTEIN DETERMINED AT LOWER RESOLUTION (PDB ID 3GWP), A BOUND COFACTOR PYRIDOXAL-5'-PHOSPHATE (PLP) AND LYS 243 AT THE ACTIVE SITE WERE MODELED AS N'-PYRIDOXYL-LYSINE-5'-MONOPHOSPHATE (LLP). IN THIS STRUCTURE, A PLP COFACTOR WAS MODELED INTO THE B-SUBUNIT ONLY. SOME OF ELECTRON DENSITIES IN THE VICINITY OF THE ACTIVE SITES ON THE OTHER THREE SUBUNITS WERE MODELED AS L(+)-TARTARIC ACID (TLA), USED AS A BUFFER IN THE CRYSTALLIZATION. 6). ANALYSIS WITH THE MOLPROBITY VALIDATION SERVER SHOWS THAT GLY 380 ON THE A, C, AND D SUBUNITS ARE RAMACHANDRAN OUTLIERS EVEN THOUGH ELECTRON DENSITY SUPPORTS THEIR POSITIONING. 7). ELECTRON DENSITY BETWEEN RESIDUES 369-371 ON THE A SUBUNIT IS DISORDERED AND THESE RESIDUES COULD NOT BE RELIABLY MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.206 6076 5 %RANDOM
Rwork0.165 ---
obs0.168 120713 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å20 Å2
2---0.6 Å20 Å2
3---1.2 Å2
Refinement stepCycle: LAST / Resolution: 2→29.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13080 0 124 1004 14208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02213672
X-RAY DIFFRACTIONr_bond_other_d0.0020.029315
X-RAY DIFFRACTIONr_angle_refined_deg1.4651.97518480
X-RAY DIFFRACTIONr_angle_other_deg0.986322843
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.47951779
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.63124.884602
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.319152418
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7821568
X-RAY DIFFRACTIONr_chiral_restr0.0890.22072
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215337
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022674
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.42838539
X-RAY DIFFRACTIONr_mcbond_other0.4133555
X-RAY DIFFRACTIONr_mcangle_it2.382513763
X-RAY DIFFRACTIONr_scbond_it4.35585133
X-RAY DIFFRACTIONr_scangle_it6.268114676
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A4353medium positional0.180.5
B4353medium positional0.290.5
C4353medium positional0.220.5
D4353medium positional0.210.5
A731loose positional0.685
B731loose positional1.515
C731loose positional0.655
D731loose positional0.695
A4353medium thermal1.942
B4353medium thermal2.082
C4353medium thermal1.882
D4353medium thermal1.862
A731loose thermal3.0410
B731loose thermal5.3210
C731loose thermal3.210
D731loose thermal4.710
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 458 -
Rwork0.251 8389 -
obs--99.8 %
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)
11.2104-0.1126-0.56790.51620.27380.7869-0.0816-0.0516-0.32170.143-0.06320.0760.2083-0.06020.14490.1482-0.04810.00730.0556-0.030.1611-4.97724.86469.411
20.74920.35620.19420.53060.27170.65140.02440.06030.0358-0.05320.0117-0.02670.02260.0599-0.03610.07380.04380.01220.0485-0.02430.072422.22141.33452.967
30.66260.1198-0.2240.46910.00110.78790.0275-0.0966-0.02870.0543-0.0045-0.1267-0.00630.1558-0.0230.02310.001-0.01790.0546-0.02370.057224.28367.11385.865
40.61240.3248-0.06161.0669-0.03860.4140.0106-0.0385-0.01370.0177-0.00640.15320.0291-0.1102-0.00430.03650.0030.00950.0943-0.0110.0372-10.20359.79192.07
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 426
2X-RAY DIFFRACTION2B0 - 426
3X-RAY DIFFRACTION3C0 - 426
4X-RAY DIFFRACTION4D0 - 426

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