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- PDB-3cvj: Crystal structure of a putative phosphoheptose isomerase (bh3325)... -

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Entry
Database: PDB / ID: 3cvj
TitleCrystal structure of a putative phosphoheptose isomerase (bh3325) from bacillus halodurans c-125 at 2.00 A resolution
ComponentsPutative phosphoheptose isomerase
KeywordsISOMERASE / Rossmann fold / 3-layer (aba) sandwich / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


carbohydrate derivative metabolic process / carbohydrate derivative binding
Similarity search - Function
Uncharacterised protein family UPF0309 / RpiR-like, SIS domain / SIS domain / SIS domain / SIS domain profile. / Glucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / UPF0309 protein BH3325
Similarity search - Component
Biological speciesBacillus halodurans C-125 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative phosphoheptose isomerase (NP_244191.1) from Bacillus halodurans at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Oct 25, 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 1.5Feb 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.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_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: Putative phosphoheptose isomerase
B: Putative phosphoheptose isomerase
C: Putative phosphoheptose isomerase
D: Putative phosphoheptose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,58615
Polymers108,9914
Non-polymers59511
Water7,458414
1
A: Putative phosphoheptose isomerase
B: Putative phosphoheptose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7627
Polymers54,4962
Non-polymers2675
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-45.4 kcal/mol
Surface area18180 Å2
MethodPISA
2
C: Putative phosphoheptose isomerase
D: Putative phosphoheptose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8248
Polymers54,4962
Non-polymers3296
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-47.7 kcal/mol
Surface area17800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.490, 83.430, 183.770
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

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: SER / End label comp-ID: LYS / Refine code: 5 / Auth seq-ID: 3 - 241 / Label seq-ID: 4 - 242

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
DetailsCRYSTAL PACKING ANALYSIS SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein
Putative phosphoheptose isomerase / UPF0309 protein BH3325


Mass: 27247.760 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans C-125 (bacteria) / Species: Bacillus halodurans / Strain: C-125 / DSM 18197 / FERM 7344 / JCM 9153 / Gene: NP_244191.1, BH3325 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9K7N6
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 414 / 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: 2.02 Å3/Da / Density % sol: 39.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.33
Details: NANODROP, 22.0% PEG 8000, 0.15M Magnesium acetate, 0.1M Sodium cacodylate pH 6.33, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97854 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 3, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97854 Å / Relative weight: 1
ReflectionResolution: 2→29.566 Å / Num. obs: 60439 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.086 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 9.96
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2-2.070.8881.43505811123198.4
2.07-2.150.6811.93552711144199.7
2.15-2.250.4832.63765111809199.5
2.25-2.370.3763.33726011655199.7
2.37-2.520.2644.63751711640199.7
2.52-2.710.1816.53619711255199.8
2.71-2.990.1239.23832311839199.8
2.99-3.420.07214.73693011423199.7
3.42-4.30.0424.53690311459199.8
4.3-29.5660.02931.13650011351197.5

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0069refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.004data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2→29.566 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 9.29 / SU ML: 0.13 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.169
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN 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 RECORDS CONTAIN 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. MAGNESIUM (MG) AND ACETATE (ACT) IONS FROM CRYSTALLIZATION AND ETHYLENE GLYCOL (EDO) FROM CRYO SOLUTION WERE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.221 3060 5.1 %RANDOM
Rwork0.174 ---
obs0.176 60380 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.606 Å2
Baniso -1Baniso -2Baniso -3
1--2.13 Å20 Å20 Å2
2--2.03 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2→29.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7465 0 38 414 7917
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0227839
X-RAY DIFFRACTIONr_bond_other_d0.0010.025188
X-RAY DIFFRACTIONr_angle_refined_deg1.531.94810619
X-RAY DIFFRACTIONr_angle_other_deg1.487312705
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1451006
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.85524.54348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.981151335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7751536
X-RAY DIFFRACTIONr_chiral_restr0.0860.21185
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028904
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021576
X-RAY DIFFRACTIONr_mcbond_it1.05824936
X-RAY DIFFRACTIONr_mcbond_other0.32822022
X-RAY DIFFRACTIONr_mcangle_it1.6837960
X-RAY DIFFRACTIONr_scbond_it1.50722903
X-RAY DIFFRACTIONr_scangle_it2.03232659
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1331MEDIUM POSITIONAL0.20.5
2B1331MEDIUM POSITIONAL0.160.5
3C1331MEDIUM POSITIONAL0.230.5
4D1331MEDIUM POSITIONAL0.160.5
1A1479LOOSE POSITIONAL0.415
2B1479LOOSE POSITIONAL0.465
3C1479LOOSE POSITIONAL0.385
4D1479LOOSE POSITIONAL0.375
1A1331MEDIUM THERMAL0.82
2B1331MEDIUM THERMAL0.772
3C1331MEDIUM THERMAL0.842
4D1331MEDIUM THERMAL0.762
1A1479LOOSE THERMAL0.710
2B1479LOOSE THERMAL0.8110
3C1479LOOSE THERMAL0.8310
4D1479LOOSE THERMAL0.7110
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 245 -
Rwork0.246 4117 -
all-4362 -
obs--98.35 %
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)
11.4559-0.09190.07380.7601-0.25640.5391-0.0416-0.0873-0.1320.0150.01030.10560.0225-0.03870.0313-0.10180.00150.0407-0.03350.0631-0.05745.669217.849434.9441
21.3740.0766-0.08770.9367-0.20.75-0.0466-0.1576-0.00440.09840.02230.0357-0.0420.01550.0244-0.09380.02430.0053-0.07110.0689-0.078125.503121.023636.878
30.87770.01930.0231.0793-0.22761.69170.01590.00140.15230.05970.04890.2434-0.2529-0.0909-0.0648-0.0170.0277-0.0388-0.10280.07060.025510.059751.749416.1105
40.81930.06740.11060.7714-0.08360.79590.02610.17760.0015-0.1497-0.04370.0406-0.06930.06410.0176-0.0281-0.0195-0.0385-0.03420.0703-0.069618.951739.32183.1257
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 2421 - 243
2X-RAY DIFFRACTION2BB0 - 2421 - 243
3X-RAY DIFFRACTION3CC1 - 2422 - 243
4X-RAY DIFFRACTION4DD1 - 2422 - 243

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