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- PDB-3eua: CRYSTAL STRUCTURE OF A PUTATIVE PHOSPHOSUGAR ISOMERASE (BSU32610)... -

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Basic information

Entry
Database: PDB / ID: 3eua
TitleCRYSTAL STRUCTURE OF A PUTATIVE PHOSPHOSUGAR ISOMERASE (BSU32610) FROM BACILLUS SUBTILIS AT 1.90 A RESOLUTION
ComponentsPUTATIVE FRUCTOSE-AMINOACID-6-PHOSPHATE DEGLYCASE
KeywordsISOMERASE / PUTATIVE PHOSPHOSUGAR ISOMERASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds / glutamine-fructose-6-phosphate transaminase (isomerizing) activity / UDP-N-acetylglucosamine metabolic process / carbohydrate derivative binding / fructose 6-phosphate metabolic process / protein N-linked glycosylation / carbohydrate metabolic process / hydrolase activity / cytosol
Similarity search - Function
Arc Repressor Mutant, subunit A - #2240 / Rossmann fold - #12570 / Fructosamine deglycase FrlB / Fructosamine deglycase FrlB, SIS domain 1 / GlmS/FrlB, SIS domain 2 / SIS domain / SIS domain / SIS domain profile. / Glucose-6-phosphate isomerase like protein; domain 1 / Arc Repressor Mutant, subunit A ...Arc Repressor Mutant, subunit A - #2240 / Rossmann fold - #12570 / Fructosamine deglycase FrlB / Fructosamine deglycase FrlB, SIS domain 1 / GlmS/FrlB, SIS domain 2 / SIS domain / SIS domain / SIS domain profile. / Glucose-6-phosphate isomerase like protein; domain 1 / Arc Repressor Mutant, subunit A / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / Fructosamine deglycase FrlB
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of yurp protein (np_391141.1) from bacillus subtilis at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 9, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: 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: PUTATIVE FRUCTOSE-AMINOACID-6-PHOSPHATE DEGLYCASE
B: PUTATIVE FRUCTOSE-AMINOACID-6-PHOSPHATE DEGLYCASE
C: PUTATIVE FRUCTOSE-AMINOACID-6-PHOSPHATE DEGLYCASE
D: PUTATIVE FRUCTOSE-AMINOACID-6-PHOSPHATE DEGLYCASE
E: PUTATIVE FRUCTOSE-AMINOACID-6-PHOSPHATE DEGLYCASE
F: PUTATIVE FRUCTOSE-AMINOACID-6-PHOSPHATE DEGLYCASE
G: PUTATIVE FRUCTOSE-AMINOACID-6-PHOSPHATE DEGLYCASE
H: PUTATIVE FRUCTOSE-AMINOACID-6-PHOSPHATE DEGLYCASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)298,97912
Polymers298,4168
Non-polymers5624
Water30,6621702
1
A: PUTATIVE FRUCTOSE-AMINOACID-6-PHOSPHATE DEGLYCASE
B: PUTATIVE FRUCTOSE-AMINOACID-6-PHOSPHATE DEGLYCASE


Theoretical massNumber of molelcules
Total (without water)74,6042
Polymers74,6042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-18 kcal/mol
Surface area23000 Å2
MethodPISA
2
C: PUTATIVE FRUCTOSE-AMINOACID-6-PHOSPHATE DEGLYCASE
D: PUTATIVE FRUCTOSE-AMINOACID-6-PHOSPHATE DEGLYCASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8854
Polymers74,6042
Non-polymers2812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6720 Å2
ΔGint-17 kcal/mol
Surface area23110 Å2
MethodPISA
3
E: PUTATIVE FRUCTOSE-AMINOACID-6-PHOSPHATE DEGLYCASE
F: PUTATIVE FRUCTOSE-AMINOACID-6-PHOSPHATE DEGLYCASE


Theoretical massNumber of molelcules
Total (without water)74,6042
Polymers74,6042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-18 kcal/mol
Surface area23450 Å2
MethodPISA
4
G: PUTATIVE FRUCTOSE-AMINOACID-6-PHOSPHATE DEGLYCASE
H: PUTATIVE FRUCTOSE-AMINOACID-6-PHOSPHATE DEGLYCASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8854
Polymers74,6042
Non-polymers2812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-17 kcal/mol
Surface area23530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.857, 91.822, 119.041
Angle α, β, γ (deg.)109.300, 100.450, 96.550
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 2 / Auth seq-ID: 5 - 328 / Label seq-ID: 5 - 328

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH

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Components

#1: Protein
PUTATIVE FRUCTOSE-AMINOACID-6-PHOSPHATE DEGLYCASE


Mass: 37302.055 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: NP_391141.1, BSU32610, yurP / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: O32157
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1702 / 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: 2.03 Å3/Da / Density % sol: 39.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 15.0% Glycerol, 0.1700M NH4OAc, 25.5% PEG-4000, 0.1M Citrate pH 5.6, 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: 0.91837,0.97908,0.97864
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 17, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979081
30.978641
ReflectionResolution: 1.9→29.975 Å / Num. obs: 179677 / % possible obs: 97.1 % / Redundancy: 2 % / Biso Wilson estimate: 18.965 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 7.179
Reflection shell

Diffraction-ID: 1 / Redundancy: 2 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-1.950.421.625900131170.4295.9
1.95-20.3442.125286127910.34496.1
2-2.060.2872.524753125140.28796.3
2.06-2.120.2332.424151122090.23396.4
2.12-2.190.1933.823310117800.19396.5
2.19-2.270.172222651114520.17296.7
2.27-2.360.1484.921877110690.14896.9
2.36-2.450.1335.521001106140.13397
2.45-2.560.1116.520325102760.11197.1
2.56-2.690.0927.81926097340.09297.2
2.69-2.830.0878.11848493450.08797.5
2.83-30.0739.41748688340.07397.6
3-3.210.05911.51651183510.05997.7
3.21-3.470.053121521776980.05397.9
3.47-3.80.04513.51417371790.04598.1
3.8-4.250.04114.81276564520.04198.1
4.25-4.910.039151126056860.03998.3
4.91-6.010.04213.3957048460.04298.4
6.01-8.50.04312.5737537320.04398.7
8.5-29.980.03513.9393319980.03596.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→29.975 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 7.238 / SU ML: 0.106 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.15
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS 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 RECORD CONTAINS 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.CITRATE ANIONS AND GLYCEROL MOLECULES FROM CRYSTALLIZATION ARE MODELED INTO THIS STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.212 8990 5 %RANDOM
Rwork0.168 ---
obs0.17 179676 97.07 %-
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 max: 65.07 Å2 / Biso mean: 23.585 Å2 / Biso min: 9.08 Å2
Baniso -1Baniso -2Baniso -3
1-1.2 Å20.93 Å2-0.04 Å2
2--0.14 Å2-0.11 Å2
3----1.22 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20474 0 38 1702 22214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02221210
X-RAY DIFFRACTIONr_bond_other_d0.0030.0214012
X-RAY DIFFRACTIONr_angle_refined_deg1.6471.9528783
X-RAY DIFFRACTIONr_angle_other_deg1.165334224
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.83552647
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.15424.555988
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.465153531
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9651585
X-RAY DIFFRACTIONr_chiral_restr0.0880.23153
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0223958
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024379
X-RAY DIFFRACTIONr_nbd_refined0.210.34621
X-RAY DIFFRACTIONr_nbd_other0.1820.315025
X-RAY DIFFRACTIONr_nbtor_refined0.1850.510625
X-RAY DIFFRACTIONr_nbtor_other0.0950.510181
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.52666
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1640.56
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2520.337
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2060.373
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2350.554
X-RAY DIFFRACTIONr_mcbond_it0.7891.513641
X-RAY DIFFRACTIONr_mcbond_other0.1911.55321
X-RAY DIFFRACTIONr_mcangle_it1.098221050
X-RAY DIFFRACTIONr_scbond_it2.10138922
X-RAY DIFFRACTIONr_scangle_it2.9764.57733
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1819TIGHT POSITIONAL0.050.05
2B1819TIGHT POSITIONAL0.050.05
3C1819TIGHT POSITIONAL0.050.05
4D1819TIGHT POSITIONAL0.070.05
5E1819TIGHT POSITIONAL0.060.05
6F1819TIGHT POSITIONAL0.060.05
7G1819TIGHT POSITIONAL0.060.05
8H1819TIGHT POSITIONAL0.060.05
1A2106MEDIUM POSITIONAL0.30.5
2B2106MEDIUM POSITIONAL0.350.5
3C2106MEDIUM POSITIONAL0.260.5
4D2106MEDIUM POSITIONAL0.370.5
5E2106MEDIUM POSITIONAL0.330.5
6F2106MEDIUM POSITIONAL0.290.5
7G2106MEDIUM POSITIONAL0.330.5
8H2106MEDIUM POSITIONAL0.30.5
1A1819TIGHT THERMAL0.150.5
2B1819TIGHT THERMAL0.130.5
3C1819TIGHT THERMAL0.140.5
4D1819TIGHT THERMAL0.160.5
5E1819TIGHT THERMAL0.170.5
6F1819TIGHT THERMAL0.180.5
7G1819TIGHT THERMAL0.160.5
8H1819TIGHT THERMAL0.160.5
1A2106MEDIUM THERMAL0.632
2B2106MEDIUM THERMAL0.652
3C2106MEDIUM THERMAL0.642
4D2106MEDIUM THERMAL0.662
5E2106MEDIUM THERMAL0.742
6F2106MEDIUM THERMAL0.752
7G2106MEDIUM THERMAL0.722
8H2106MEDIUM THERMAL0.712
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 616 -
Rwork0.23 12444 -
all-13060 -
obs--95.95 %
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)
10.57390.0023-0.46880.351-0.26021.4507-0.00580.02260.00720.00310.03510.0055-0.0585-0.0121-0.02930.00160.0107-0.0024-0.0505-0.0129-0.040723.825642.716748.51
20.7468-0.2115-0.42720.3688-0.13161.0734-0.107-0.1009-0.08750.10540.10370.10350.0528-0.03220.00330.04520.04470.0269-0.00910.0195-0.012513.582334.491170.775
30.3292-0.19210.06810.5097-0.33821.5487-0.0214-0.0677-0.04130.02090.10070.0387-0.0497-0.1643-0.0793-0.05630.00640.001-0.01920.0032-0.01649.2464-11.542270.4752
40.22770.12760.15970.2815-0.41961.9558-0.04060.04110.0056-0.05420.0274-0.0391-0.18190.14390.01330.0037-0.03190.0023-0.0417-0.0216-0.016858.3816-2.341248.1841
50.54920.2161-0.03280.4169-0.02890.3176-0.08070.08330.0289-0.10270.07350.02150.0414-0.01590.0072-0.0343-0.0458-0.0156-0.03750.0009-0.033233.631935.2227103.1774
60.5381-0.1550.00760.2781-0.01680.1404-0.0562-0.09730.07640.04360.0542-0.0480.00120.02820.0021-0.0563-0.0031-0.0284-0.036-0.0238-0.004745.167245.4486124.1569
70.26920.13730.18020.36830.21270.8685-0.04550.0428-0.0041-0.05040.03030.02270.051-0.05590.0152-0.0641-0.03040.0029-0.0207-0.0072-0.015969.7988-10.0482102.6028
80.3845-0.0980.14250.38540.03210.4617-0.0398-0.02530.02060.05290.0224-0.0349-0.0080.02180.0174-0.0703-0.006-0.0119-0.045-0.0084-0.012880.7536-0.2326124.0473
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 328
2X-RAY DIFFRACTION2B5 - 328
3X-RAY DIFFRACTION3C5 - 328
4X-RAY DIFFRACTION4D5 - 328
5X-RAY DIFFRACTION5E5 - 328
6X-RAY DIFFRACTION6F0 - 328
7X-RAY DIFFRACTION7G1 - 328
8X-RAY DIFFRACTION8H3 - 328

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