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- PDB-2q02: Crystal structure of a xylose isomerase domain containing protein... -

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Basic information

Entry
Database: PDB / ID: 2q02
TitleCrystal structure of a xylose isomerase domain containing protein (stm4435) from salmonella typhimurium lt2 at 2.40 A resolution
ComponentsPutative cytoplasmic proteinCytoplasm
KeywordsUNKNOWN FUNCTION / Putative cytoplasmic protein / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


racemase and epimerase activity, acting on carbohydrates and derivatives / manganese ion binding
Similarity search - Function
Uncharacterised conserved protein UCP036778, sugar epimerase-type / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Unknown ligand / Cytoplasmic protein
Similarity search - Component
Biological speciesSalmonella typhimurium LT2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative cytoplasmic protein (NP_463296.1) from Salmonella typhimurium LT2 at 2.40 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jul 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 1.5Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_conn_type / 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_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE 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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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative cytoplasmic protein
B: Putative cytoplasmic protein
C: Putative cytoplasmic protein
D: Putative cytoplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,08622
Polymers124,4104
Non-polymers67618
Water4,252236
1
A: Putative cytoplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3046
Polymers31,1031
Non-polymers2025
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Putative cytoplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3407
Polymers31,1031
Non-polymers2376
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: Putative cytoplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2395
Polymers31,1031
Non-polymers1364
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: Putative cytoplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2034
Polymers31,1031
Non-polymers1013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
A: Putative cytoplasmic protein
hetero molecules

C: Putative cytoplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,54311
Polymers62,2052
Non-polymers3389
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y+1/2,-z+1/21
Buried area2460 Å2
ΔGint-154 kcal/mol
Surface area22290 Å2
MethodPISA
6
B: Putative cytoplasmic protein
hetero molecules

D: Putative cytoplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,54311
Polymers62,2052
Non-polymers3389
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x+1/2,-y+3/2,-z+11
Buried area2470 Å2
ΔGint-158 kcal/mol
Surface area22050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.500, 95.230, 136.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D
91A
101B
111C
121D

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg label comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYPHE2AA0 - 751 - 76
21GLYPHE2BB0 - 751 - 76
31MSEPHE2CC1 - 752 - 76
41GLYPHE2DD0 - 751 - 76
52LEULEU2AA89 - 17590 - 176
62LEULEU2BB89 - 17590 - 176
72LEULEU2CC89 - 17590 - 176
82LEULEU2DD89 - 17590 - 176
93ILEGLN4AA187 - 271188 - 272
103ILEGLN4BB187 - 271188 - 272
113ILEGLN4CC187 - 271188 - 272
123ILEGLN4DD187 - 271188 - 272

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Components

#1: Protein
Putative cytoplasmic protein / Cytoplasm


Mass: 31102.584 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium LT2 (bacteria)
Species: Salmonella typhimuriumSalmonella enterica subsp. enterica
Strain: LT2, SGSC1412 / Gene: NP_463296.1, STM4435 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8ZK48
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 4 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: NANODROP, 20.0% Glycerol, 0.16M Mg(OAc)2, 16.0% PEG 8000, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91162, 0.97922, 0.97894
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 12, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979221
30.978941
ReflectionResolution: 2.4→29.386 Å / Num. obs: 48661 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 44.32 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 9.83
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.4-2.490.3222.415045908092.4
2.49-2.580.2832.814220842899.8
2.58-2.70.2373.615493952298.8
2.7-2.840.1884.315623920299.8
2.84-3.020.1375.816352953999.8
3.02-3.250.1027.815959926499.7
3.25-3.580.06911.215666939899.1
3.58-4.090.04815.914889917698.3
4.09-5.140.03320.816275935499.7
5.140.0252316814942498.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→29.386 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / SU B: 17.462 / SU ML: 0.206 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.407 / ESU R Free: 0.244
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 RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. DATA HAS PARTIAL-MEROHEDRAL TWINNING, WITH TWIN OPERATOR -K,-H,-L AND AN APPARENT TWIN FRACTION OF 10%. DATA WAS NOT DETWINNED DURING REFINEMENT. 5. THE R-FREE SET WAS GENERATED USING THE TWIN LAWS. 6. ZINC WAS MODELED BASED ON GEOMETRY AND COORDINATION ENVIRONMENT, AND CONFIRMED WITH X-RAY FLUORESCENCE AND ANOMALOUS DIFFERENCE FOURIER EXPERIMENTS. 7. CHLORINE ATOMS WERE MODELED BASED ON CRYSTALLIZATION CONDITIONS. 8. UNKNOWN LIGANDS (UNL) WERE MODELED BASED ON LOCATION OF PROPOSED ACTIVE SITE. 9. THERE IS AN UNMODELED DIFFERENCE DENSITY NEAR ARG A148.
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2435 5 %RANDOM
Rwork0.184 ---
obs0.186 48605 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.088 Å2
Baniso -1Baniso -2Baniso -3
1--1.36 Å20 Å20 Å2
2---1.38 Å20 Å2
3---2.74 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8552 0 27 236 8815
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0228753
X-RAY DIFFRACTIONr_bond_other_d0.0020.028097
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.96811859
X-RAY DIFFRACTIONr_angle_other_deg0.82318722
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9951095
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.11224.172429
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.895151512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1841573
X-RAY DIFFRACTIONr_chiral_restr0.0710.21354
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029820
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021781
X-RAY DIFFRACTIONr_nbd_refined0.2140.21818
X-RAY DIFFRACTIONr_nbd_other0.180.28319
X-RAY DIFFRACTIONr_nbtor_refined0.1750.24243
X-RAY DIFFRACTIONr_nbtor_other0.0840.25124
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2245
X-RAY DIFFRACTIONr_metal_ion_refined0.070.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2280.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1040.29
X-RAY DIFFRACTIONr_mcbond_it1.11435975
X-RAY DIFFRACTIONr_mcbond_other0.43332207
X-RAY DIFFRACTIONr_mcangle_it1.53358766
X-RAY DIFFRACTIONr_scbond_it3.50483576
X-RAY DIFFRACTIONr_scangle_it4.625113087
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A948TIGHT POSITIONAL0.050.05
2B948TIGHT POSITIONAL0.040.05
3C948TIGHT POSITIONAL0.050.05
4D948TIGHT POSITIONAL0.050.05
1A2749MEDIUM POSITIONAL0.280.5
2B2749MEDIUM POSITIONAL0.30.5
3C2749MEDIUM POSITIONAL0.260.5
4D2749MEDIUM POSITIONAL0.30.5
1A948TIGHT THERMAL0.10.5
2B948TIGHT THERMAL0.110.5
3C948TIGHT THERMAL0.110.5
4D948TIGHT THERMAL0.10.5
1A2749MEDIUM THERMAL0.632
2B2749MEDIUM THERMAL0.712
3C2749MEDIUM THERMAL0.642
4D2749MEDIUM THERMAL0.652
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 186 -
Rwork0.251 3230 -
obs-3416 96.44 %
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)
12.6942-0.5256-0.31912.0677-0.88191.5933-0.022-0.16850.0571-0.035-0.1191-0.12280.26480.40980.1411-0.06760.09210.0437-0.00080.0589-0.118567.06284.18736.06
21.5182-0.27740.84213.59240.01632.0047-0.1713-0.09830.1349-0.00230.03070.1307-0.4175-0.49190.1407-0.05560.1095-0.0386-0.0398-0.0369-0.096658.70990.73467.114
31.6212-0.03550.10241.99030.04491.20980.0029-0.0957-0.26910.2312-0.0235-0.03670.17830.0850.0206-0.13210.01780.0082-0.17940.0168-0.100852.44546.54565.169
42.9220.4042-0.36361.186-0.16411.6362-0.07720.35440.3497-0.08550.04690.2071-0.0495-0.33040.0303-0.13770.0154-0.0084-0.10010.0445-0.035223.09677.12737.038
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA10 - 27111 - 272
2X-RAY DIFFRACTION2BB0 - 2711 - 272
3X-RAY DIFFRACTION3CC1 - 2712 - 272
4X-RAY DIFFRACTION4DD0 - 2711 - 272

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