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- PDB-3r8e: Crystal structure of a putative sugar kinase (CHU_1875) from Cyto... -

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Basic information

Entry
Database: PDB / ID: 3r8e
TitleCrystal structure of a putative sugar kinase (CHU_1875) from Cytophaga hutchinsonii ATCC 33406 at 1.65 A resolution
ComponentsHypothetical sugar kinase
KeywordsTRANSFERASE / Ribonuclease H-like motif / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-biology
Function / homology
Function and homology information


glucokinase / glucokinase activity
Similarity search - Function
ROK family signature. / ROK family / ROK family / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Glucokinase / Glucokinase
Similarity search - Component
Biological speciesCytophaga hutchinsonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Hypothetical sugar kinase (CHU_1875) from CYTOPHAGA HUTCHINSONII ATCC 33406 at 1.65 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 24, 2014Group: Structure summary
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical sugar kinase


Theoretical massNumber of molelcules
Total (without water)35,3271
Polymers35,3271
Non-polymers00
Water3,729207
1
A: Hypothetical sugar kinase

A: Hypothetical sugar kinase


Theoretical massNumber of molelcules
Total (without water)70,6542
Polymers70,6542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3060 Å2
ΔGint-16 kcal/mol
Surface area24870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.827, 78.359, 65.744
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-423-

HOH

DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Hypothetical sugar kinase


Mass: 35326.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cytophaga hutchinsonii (bacteria) / Strain: ATCC 33406 / Gene: glk, CHU_1875 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q11TX3, UniProt: A0A6N4SS40*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.62 Å3/Da / Density % sol: 53.03 % / Mosaicity: 0.24 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30% polyethylene glycol 3350, 0.2M sodium citrate, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97919
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 26, 2010
Details: Vertical focusing mirror; double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.65→29.89 Å / Num. all: 45238 / Num. obs: 45238 / % possible obs: 99.7 % / Redundancy: 4.9 % / Rpim(I) all: 0.05 / Rrim(I) all: 0.111 / Rsym value: 0.099 / Net I/av σ(I): 4.691 / Net I/σ(I): 7.9 / Num. measured all: 219449
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.65-1.694.60.850.75411455231750.3870.850.7541.996.3
1.69-1.744.90.7360.6581.21582532470.3240.7360.6582.2100
1.74-1.794.90.5760.5151.51517831090.2550.5760.5152.7100
1.79-1.844.90.4620.4121.91488830510.2050.4620.4123.2100
1.84-1.914.90.3780.3372.21448729580.1680.3780.3373.9100
1.91-1.974.90.3050.2722.81402128710.1360.3050.2724.7100
1.97-2.054.90.2380.2123.51371227890.1060.2380.2125.8100
2.05-2.134.90.2070.1843.91305026610.0930.2070.1846.7100
2.13-2.224.90.1730.1544.31259225580.0780.1730.1547.7100
2.22-2.334.90.1510.1345.11207524570.0680.1510.1348.6100
2.33-2.464.90.1340.1195.71148023410.0610.1340.1199.7100
2.46-2.614.90.1220.10861092922220.0550.1220.10810.4100
2.61-2.794.90.1150.1026.41022020980.0520.1150.10211.5100
2.79-3.014.90.110.0986.6963019600.050.110.09812.9100
3.01-3.34.90.090.087.9880518020.0410.090.0814.4100
3.3-3.694.90.0790.079800616490.0360.0790.0716.5100
3.69-4.264.80.0770.0689.2708514680.0350.0770.06817.5100
4.26-5.224.70.0720.0649.9594512520.0320.0720.06418.6100
5.22-7.384.60.0850.0768.5463410000.0390.0850.07617100
7.38-29.8914.10.0760.06610.223355700.0360.0760.06617.597

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SOLVEphasing
SCALA3.3.15data scaling
BUSTER-TNT2.8.0refinement
Xpleo0.9.0.2model building
MOSFLMdata reduction
BUSTER2.8.0refinement
RefinementMethod to determine structure: SAD / Resolution: 1.65→29.89 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.9335 / Occupancy max: 1 / Occupancy min: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 2. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE ...Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 2. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 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. SAD PHASE RESTRAINTS (HL COEFFICIENTS) WERE USED DURING THE REFINEMENT. 5. THREE REGIONS (RESIDUES 8-12, 27-51, AND 66-90) WERE MODELED IN TWO CONFORMATIONS USING THE PROGRAM XPLEO.
RfactorNum. reflection% reflectionSelection details
Rfree0.2346 2280 5.05 %RANDOM
Rwork0.2137 ---
obs0.2147 45182 --
Displacement parametersBiso max: 120.57 Å2 / Biso mean: 34.6557 Å2 / Biso min: 9.06 Å2
Baniso -1Baniso -2Baniso -3
1-1.1394 Å20 Å20 Å2
2--2.4807 Å20 Å2
3----3.6201 Å2
Refinement stepCycle: LAST / Resolution: 1.65→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2249 0 0 207 2456
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1279SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes58HARMONIC2
X-RAY DIFFRACTIONt_gen_planes415HARMONIC5
X-RAY DIFFRACTIONt_it2764HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion373SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3528SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2764HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg3765HARMONIC21.02
X-RAY DIFFRACTIONt_omega_torsion2.95
X-RAY DIFFRACTIONt_other_torsion2.92
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2304 149 4.71 %
Rwork0.2276 3017 -
all0.2277 3166 -
Refinement TLS params.Method: refined / Origin x: 14.9712 Å / Origin y: 10.8044 Å / Origin z: 18.6762 Å
111213212223313233
T-0.1434 Å2-0.0088 Å20.0478 Å2--0.1438 Å2-0.0192 Å2---0.0075 Å2
L1.161 °2-0.0768 °20.1264 °2-2.0945 °20.1565 °2--0.3884 °2
S0.0603 Å °0.0992 Å °0.1776 Å °-0.0908 Å °0.0627 Å °-0.4793 Å °-0.0461 Å °0.0774 Å °-0.123 Å °
Refinement TLS groupSelection details: { A|0 - A|300 }

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