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- PDB-2r3e: CRYSTAL STRUCTURE OF a ribokinase-like superfamily protein (EF179... -

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Basic information

Entry
Database: PDB / ID: 2r3e
TitleCRYSTAL STRUCTURE OF a ribokinase-like superfamily protein (EF1790) FROM ENTEROCOCCUS FAECALIS V583 AT 1.95 A RESOLUTION
ComponentsYjeF-related protein
KeywordsTRANSFERASE / PUTATIVE KINASE IN THE RIBOKINASE-LIKE SUPERFAMILY / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


ADP-dependent NAD(P)H-hydrate dehydratase / ADP-dependent NAD(P)H-hydrate dehydratase activity / nicotinamide nucleotide metabolic process / ATP binding
Similarity search - Function
YjeF C-terminal domain signature 1. / Carbohydrate kinase, predicted, conserved site / YjeF C-terminal domain signature 2. / ATP/ADP-dependent (S)-NAD(P)H-hydrate dehydratase / Carbohydrate kinase / YjeF C-terminal domain profile. / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADP-dependent (S)-NAD(P)H-hydrate dehydratase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative kinase in the ribokinase-like superfamily from Enterococcus faecalis V583 (NP_815490.1) at 1.95 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / 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 1.4Jan 25, 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
Revision 1.5Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Remark 300 BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION ... BIOMOLECULE: 1 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. SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A TETRAMER AS A SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YjeF-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5693
Polymers34,4451
Non-polymers1242
Water2,558142
1
A: YjeF-related protein
hetero molecules

A: YjeF-related protein
hetero molecules

A: YjeF-related protein
hetero molecules

A: YjeF-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,27612
Polymers137,7804
Non-polymers4978
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area11190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.888, 109.888, 54.193
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A TETRAMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein YjeF-related protein


Mass: 34444.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: NP_815490.1, EF_1790 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q833Y3
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.37 Å3/Da / Density % sol: 48.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: NANODROP, 10.0% PEG 6000, 0.1M Bicine pH 9.0, 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: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 1, 2007 / 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: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→27.472 Å / Num. obs: 23697 / % possible obs: 99.9 % / Redundancy: 5.4 % / Biso Wilson estimate: 37.05 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 6.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.95-25.40.6661.1949417580.666100
2-2.065.40.5011.5908216790.501100
2.06-2.125.40.3791.7903616830.379100
2.12-2.185.40.3032.4844215650.303100
2.18-2.255.40.2650.7847615750.265100
2.25-2.335.40.2140.9806014840.214100
2.33-2.425.40.1624.5796214660.162100
2.42-2.525.40.1385754813940.138100
2.52-2.635.40.1125.9737513540.112100
2.63-2.765.40.0965.9696812910.096100
2.76-2.915.40.0758.9661912200.075100
2.91-3.085.40.0699.1631211590.069100
3.08-3.35.40.0639.8596610970.063100
3.3-3.565.40.05510.5556210260.055100
3.56-3.95.40.04910.451479470.049100
3.9-4.365.40.04113.245638430.041100
4.36-5.035.40.04512.640727540.045100
5.03-6.175.40.04512.234546450.045100
6.17-8.725.30.03418.326525040.03499.9
8.72-27.4724.50.03121.511422530.03188.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2R3B

2r3b


Resolution: 1.95→27.472 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.962 / SU B: 6.15 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. ONE EDO MODELED IS PRESENT IN CRYO CONDITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.194 1216 5.1 %RANDOM
Rwork0.155 ---
all0.157 ---
obs0.157 23697 99.84 %-
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: 37.69 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å20 Å20 Å2
2---0.74 Å20 Å2
3---1.49 Å2
Refinement stepCycle: LAST / Resolution: 1.95→27.472 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2095 0 8 142 2245
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222155
X-RAY DIFFRACTIONr_bond_other_d0.0010.021417
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.9592926
X-RAY DIFFRACTIONr_angle_other_deg0.92733492
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9695279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.99824.88486
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.10815364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.811158
X-RAY DIFFRACTIONr_chiral_restr0.0850.2343
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022389
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02401
X-RAY DIFFRACTIONr_nbd_refined0.2180.2462
X-RAY DIFFRACTIONr_nbd_other0.1840.21413
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21074
X-RAY DIFFRACTIONr_nbtor_other0.0880.21054
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2129
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2430.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1030.213
X-RAY DIFFRACTIONr_mcbond_it2.18931497
X-RAY DIFFRACTIONr_mcbond_other0.523566
X-RAY DIFFRACTIONr_mcangle_it2.97152212
X-RAY DIFFRACTIONr_scbond_it5.4518848
X-RAY DIFFRACTIONr_scangle_it6.87911712
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 81 -
Rwork0.198 1680 -
obs-1761 100 %
Refinement TLS params.Method: refined / Origin x: 44.3406 Å / Origin y: 32.1618 Å / Origin z: 0.3724 Å
111213212223313233
T-0.0108 Å2-0.0206 Å20.0115 Å2--0.0532 Å2-0.0592 Å2---0.0068 Å2
L0.9296 °20.4354 °2-0.2326 °2-0.8629 °2-0.0064 °2--0.9653 °2
S-0.0492 Å °0.1138 Å °-0.2609 Å °-0.0669 Å °-0.0147 Å °0.0149 Å °0.1371 Å °-0.0761 Å °0.064 Å °
Refinement TLS groupSelection: ALL

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