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- PDB-3odp: Crystal structure of a putative tagatose-6-phosphate ketose/aldos... -

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Entry
Database: PDB / ID: 3odp
TitleCrystal structure of a putative tagatose-6-phosphate ketose/aldose isomerase (NT01CX_0292) from CLOSTRIDIUM NOVYI NT at 2.35 A resolution
Componentsputative tagatose-6-phosphate ketose/aldose isomerase
KeywordsISOMERASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homology
Function and homology information


carbohydrate derivative metabolic process / phosphoenolpyruvate-dependent sugar phosphotransferase system / carbohydrate derivative binding / isomerase activity / hydrolase activity / plasma membrane
Similarity search - Function
AgaS, SIS domain / : / GlmS/AgaS, SIS domain 1 / SIS domain / SIS domain / SIS domain profile. / SIS domain superfamily / Glucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Predicted phosphosugar isomerase
Similarity search - Component
Biological speciesClostridium novyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, MOLECULAR REPLACEMENT / SAD, molecular replacement / Resolution: 2.35 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative tagatose-6-phosphate ketose/aldose isomerase (NT01CX_0292) from CLOSTRIDIUM NOVYI NT at 2.35 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: putative tagatose-6-phosphate ketose/aldose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9974
Polymers44,5131
Non-polymers4833
Water41423
1
A: putative tagatose-6-phosphate ketose/aldose isomerase
hetero molecules

A: putative tagatose-6-phosphate ketose/aldose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,9948
Polymers89,0272
Non-polymers9676
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Unit cell
Length a, b, c (Å)89.364, 89.364, 120.012
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein putative tagatose-6-phosphate ketose/aldose isomerase / Predicted phosphosugar isomerase


Mass: 44513.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium novyi (bacteria) / Strain: NT / Gene: NT01CX_0292 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A0Q2D8
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS 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: 3.11 Å3/Da / Density % sol: 60.42 %
Description: AN INITIAL SUBSTRUCTURE SOLUTION WAS FOUND USING SHELXD AND SAD PHASES WERE REFINED WITH AUTOSHARP. AN ITERATIVE RESOLVE RUN WAS ABLE TO TRACE ~70% OF THE STRUCTURE. HOWEVER, THE ...Description: AN INITIAL SUBSTRUCTURE SOLUTION WAS FOUND USING SHELXD AND SAD PHASES WERE REFINED WITH AUTOSHARP. AN ITERATIVE RESOLVE RUN WAS ABLE TO TRACE ~70% OF THE STRUCTURE. HOWEVER, THE CONNECTIVITY OF THE RESULTING MODEL WAS POOR. MOLECULAR REPLACEMENT WITH MOLREP USING 3I0Z AS THE SEARCH MODEL PROVIDED A MORE COMPLETE STARTING MODEL FOR SUBSEQUENT MODEL BUILDING AND REFINEMENT.
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 50.00% PEG-200, 0.1M TRIS pH 7.0, NANODROP, 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: 0.97871
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 6, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97871 Å / Relative weight: 1
ReflectionResolution: 2.35→77.391 Å / Num. all: 23656 / Num. obs: 23656 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 57.921 Å2 / Rsym value: 0.084 / Net I/σ(I): 12.7
Reflection shell

Rmerge(I) obs: 0.01 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.35-2.487.50.72534633981.042100
2.48-2.637.51.22412632370.635100
2.63-2.817.41.82239030080.399100
2.81-3.037.53.12113228350.245100
3.03-3.327.45.61951926320.131100
3.32-3.727.47.11750823580.091100
3.72-4.297.48.71561421200.071100
4.29-5.257.311.51321418070.052100
5.25-7.437.214.21021614250.042100
7.43-77.3916.514.454638360.03799.8

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Phasing

PhasingMethod: SAD, molecular replacement

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Processing

Software
NameVersionClassificationNB
SHELXphasing
REFMAC5.5.0110refinement
SCALA3.3.15data scaling
PDB_EXTRACT3.1data extraction
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
autoSHARPphasing
MOLREPphasing
RefinementMethod to determine structure: SAD, MOLECULAR REPLACEMENT
Starting model: PDB entry 3I0Z

3i0z


Resolution: 2.35→77.391 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 26.475 / SU ML: 0.284 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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. 6. PEG-200 (PG4) FRAGMENTS FROM THE CRYSTALLIZATION SOLUTION ARE MODELED. 7. ASSIGNMENT OF PHOSPHATE ION (PO4) WAS BASED ON ELECTRON DENSITY AND CONSERVATION OF THE BINDING SITE IN 3I0Z AND OTHER HOMOLOG STRUCTURES. 8. THE TLS GROUPS WERE ASSIGNED WITH THE AID OF THE TLSMD SERVER. 9. THE RAMACHANDRAN OUTLIER RESIDUES 16 AND 308 ARE IN POOR DENSITY REGION.
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1215 5.1 %RANDOM
Rwork0.2278 ---
obs0.2297 23616 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 165.11 Å2 / Biso mean: 89.0472 Å2 / Biso min: 46.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20.23 Å20 Å2
2--0.47 Å20 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 2.35→77.391 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3022 0 25 23 3070
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223117
X-RAY DIFFRACTIONr_bond_other_d0.0020.022055
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.984220
X-RAY DIFFRACTIONr_angle_other_deg0.85935065
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8675397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.60425.522134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.17915540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.223159
X-RAY DIFFRACTIONr_chiral_restr0.0660.2487
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023456
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02592
X-RAY DIFFRACTIONr_mcbond_it0.3291.51956
X-RAY DIFFRACTIONr_mcbond_other0.0741.5798
X-RAY DIFFRACTIONr_mcangle_it0.60823147
X-RAY DIFFRACTIONr_scbond_it1.12131161
X-RAY DIFFRACTIONr_scangle_it1.7454.51070
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 86 -
Rwork0.339 1639 -
all-1725 -
obs--99.94 %
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)
11.8521-0.24559.13835.9402-3.6112.367-0.6285-0.22331.4126-0.0166-0.0861-1.3267-1.11640.23320.71461.3901-0.0047-1.00420.63280.3251.664917.170179.490143.64
26.42671.8170.402512.6246-0.18824.3611-0.44821.3733-0.3267-0.331-1.00710.8845-0.7444-1.12721.45530.24310.2925-0.35590.9213-0.52190.83195.581255.088546.5087
35.5202-2.79551.05892.88550.84254.6562-0.56590.6232-0.76540.366-0.56760.6268-0.0389-0.30371.13350.22330.06110.08060.3842-0.31340.923316.002642.261154.5258
44.8434-1.41090.08141.8068-0.28484.2078-0.29411.361-0.6712-0.1691-0.81330.33930.20850.33241.10740.17090.09140.02970.7782-0.20390.703924.40940.129444.9567
54.9171-2.2080.63053.8803-1.04692.3634-0.20931.7263-0.0835-0.5472-0.92620.4554-0.473-0.31521.13550.26850.1691-0.31950.8268-0.29230.673314.380551.813342.09
65.1344-2.18250.73973.1868-0.66244.2427-1.2109-0.21211.20960.9319-0.0518-0.4096-1.3905-0.2141.26270.8580.2221-0.70530.1796-0.15180.852218.904164.774964.7905
76.5893-4.8455-0.37085.48782.34185.641-0.48751.54771.5807-0.2355-0.5601-0.9358-1.18640.84591.04760.6396-0.1969-0.51880.83570.67671.12830.023664.180244.1269
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 20
2X-RAY DIFFRACTION2A21 - 49
3X-RAY DIFFRACTION3A50 - 89
4X-RAY DIFFRACTION4A90 - 140
5X-RAY DIFFRACTION5A141 - 193
6X-RAY DIFFRACTION6A194 - 356
7X-RAY DIFFRACTION7A357 - 391

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