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- PDB-2qw5: CRYSTAL STRUCTURE OF A PUTATIVE SUGAR PHOSPHATE ISOMERASE/EPIMERA... -

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Basic information

Entry
Database: PDB / ID: 2qw5
TitleCRYSTAL STRUCTURE OF A PUTATIVE SUGAR PHOSPHATE ISOMERASE/EPIMERASE (AVA4194) FROM ANABAENA VARIABILIS ATCC 29413 AT 1.78 A RESOLUTION
ComponentsXylose isomerase-like TIM barrel
KeywordsISOMERASE / PUTATIVE SUGAR PHOSPHATE ISOMERASE/EPIMERASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


isomerase activity / metal ion binding
Similarity search - Function
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
D-xylose / Xylose isomerase-like TIM barrel
Similarity search - Component
Biological speciesAnabaena variabilis ATCC 29413 (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 sugar phosphate isomerase/epimerase (YP_324688.1) from Anabaena variabilis ATCC 29413 at 1.78 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _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 1.4Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Jan 25, 2023Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 300 BIOMOLECULE: 1, 2, 3 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY ... BIOMOLECULE: 1, 2, 3 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS. AUTHORS STATE THAT THE EBI/PISA ANALYSIS SUPPORTS THE ASSIGNMENT OF A TETRAMER AS A SIGNIFICANT OLIGOMERIZATION STATE.
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: Xylose isomerase-like TIM barrel
B: Xylose isomerase-like TIM barrel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,30612
Polymers76,6062
Non-polymers70010
Water12,430690
1
A: Xylose isomerase-like TIM barrel
B: Xylose isomerase-like TIM barrel
hetero molecules

A: Xylose isomerase-like TIM barrel
B: Xylose isomerase-like TIM barrel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,61224
Polymers153,2114
Non-polymers1,40120
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area10040 Å2
MethodPISA
2
A: Xylose isomerase-like TIM barrel
hetero molecules

A: Xylose isomerase-like TIM barrel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,43414
Polymers76,6062
Non-polymers82812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3770 Å2
MethodPISA
3
B: Xylose isomerase-like TIM barrel
hetero molecules

B: Xylose isomerase-like TIM barrel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,17910
Polymers76,6062
Non-polymers5738
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.238, 84.238, 208.172
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Xylose isomerase-like TIM barrel


Mass: 38302.863 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena variabilis ATCC 29413 (bacteria)
Species: Anabaena variabilis / Strain: PCC 7937 / Gene: YP_324688.1, Ava_4194 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q3M5E3
#2: Sugar ChemComp-XLS / D-xylose / D-XYLOSE (LINEAR FORM)


Type: D-saccharide / Mass: 150.130 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H10O5

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Non-polymers , 4 types, 698 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 690 / 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: 2.41 Å3/Da / Density % sol: 48.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.1
Details: NANODROP, 0.2M CaCl2, 20.0% PEG 3350, No Buffer pH 5.1, 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: 0.91837, 0.97939
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 20, 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
10.918371
20.979391
ReflectionResolution: 1.78→42.108 Å / Num. obs: 71702 / % possible obs: 97.5 % / Biso Wilson estimate: 25.55 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 14.47
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allDiffraction-ID% possible all
1.78-1.840.6842.3262545491181
1.84-1.920.6213.1490747575197.4
1.92-20.514.2465446464198.4
2-2.110.3895.5540847465199.3
2.11-2.240.2987.1514097042199.4
2.24-2.410.2239.4518687117199.5
2.41-2.660.16712.2543607450199.7
2.66-3.040.10718.2523967223199.8
3.04-42.1080.05431.4532047419199.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
XDSdata reduction
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.78→42.108 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.321 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.122
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. RESIDUES 0-5 IN CHAIN A AND 0-6 IN CHAIN B ARE DISORDERED AND NOT INCLUDED IN THE MODEL. 4. ZN IONS ARE MODELED BASED ON THE METAL EXCITATION SCAN. 5. A GLYCEROL MOLECULE FROM THE CRYO SOLUTION IS MODELED. 6. A LIGAND MOLECULE XYLOSE IS MODELED IN EACH MONOMER.
RfactorNum. reflection% reflectionSelection details
Rfree0.224 3610 5 %RANDOM
Rwork0.177 ---
all0.179 ---
obs0.179 71600 99.03 %-
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 mean: 18.233 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å20 Å20 Å2
2---0.79 Å20 Å2
3---1.58 Å2
Refinement stepCycle: LAST / Resolution: 1.78→42.108 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5256 0 29 690 5975
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0225527
X-RAY DIFFRACTIONr_bond_other_d0.0040.023803
X-RAY DIFFRACTIONr_angle_refined_deg1.7111.9687542
X-RAY DIFFRACTIONr_angle_other_deg1.3839303
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2425680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54824.457267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.65915931
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0491530
X-RAY DIFFRACTIONr_chiral_restr0.1070.2822
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026114
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021098
X-RAY DIFFRACTIONr_nbd_refined0.1830.21065
X-RAY DIFFRACTIONr_nbd_other0.1470.23860
X-RAY DIFFRACTIONr_nbtor_refined0.1640.22720
X-RAY DIFFRACTIONr_nbtor_other0.0740.22597
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2519
X-RAY DIFFRACTIONr_metal_ion_refined0.1240.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0950.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2190.2111
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1020.245
X-RAY DIFFRACTIONr_mcbond_it2.28933817
X-RAY DIFFRACTIONr_mcbond_other0.56331305
X-RAY DIFFRACTIONr_mcangle_it2.82555428
X-RAY DIFFRACTIONr_scbond_it5.38282487
X-RAY DIFFRACTIONr_scangle_it7.218112099
LS refinement shellResolution: 1.78→1.83 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 229 -
Rwork0.308 4458 -
obs-4687 88.47 %

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