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- PDB-2r3b: CRYSTAL STRUCTURE OF a ribokinase-like superfamily protein (EF179... -

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Basic information

Entry
Database: PDB / ID: 2r3b
TitleCRYSTAL STRUCTURE OF a ribokinase-like superfamily protein (EF1790) FROM ENTEROCOCCUS FAECALIS V583 AT 1.80 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 / NAD(P)HX epimerase activity / metabolite repair / 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 / NAD(P)H-hydrate dehydratase / 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 / MAD / Resolution: 1.8 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 1.80 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: 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 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
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

Downloads & links

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Assembly

Deposited unit
A: YjeF-related protein
B: YjeF-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,60316
Polymers68,8902
Non-polymers71414
Water11,187621
1
A: YjeF-related protein
B: YjeF-related protein
hetero molecules

A: YjeF-related protein
B: YjeF-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,20732
Polymers137,7804
Non-polymers1,42728
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area10020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.817, 159.564, 102.497
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-382-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 5 / Auth seq-ID: 1 - 276 / Label seq-ID: 20 - 295

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
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.: 2
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-MG / MAGNESIUM ION


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


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 621 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.9 Å3/Da / Density % sol: 57.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: NANODROP, 0.2M MgCl2, 10.0% PEG 3000, 0.1M Cacodylate pH 6.5, 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, 0.97926, 0.97895
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 30, 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
20.979261
30.978951
ReflectionResolution: 1.8→29.591 Å / Num. obs: 73792 / % possible obs: 99.4 % / Redundancy: 5 % / Biso Wilson estimate: 20.819 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / 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
1.8-1.855.10.671.12716153650.6798.9
1.85-1.950.5131.42625752070.51398.5
1.9-1.955.10.4121.82588951240.41299
1.95-2.015.10.3512.12500849490.35198.9
2.01-2.085.10.282.72434848210.2899.3
2.08-2.1550.2273.32353246620.22799.1
2.15-2.2350.2023.72283245320.20299.2
2.23-2.3250.1674.52203643640.16799.4
2.32-2.4350.1544.82107841850.15499.6
2.43-2.5550.1285.72006639830.12899.6
2.55-2.6850.1096.61928538390.10999.7
2.68-2.8550.0987.31823736280.09899.6
2.85-3.0450.0848.11713534060.08499.8
3.04-3.2950.0719.21593531950.07199.9
3.29-3.650.05811.11465629420.05899.9
3.6-4.0250.051121331126790.051100
4.02-4.654.90.04912.41176423860.049100
4.65-5.694.90.04712.4989420190.047100
5.69-8.054.80.05212767015990.052100
8.05-29.5914.60.04412.741289070.04497.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHARPphasing
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→29.591 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.829 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.091
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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. EDO, CL AND MG MODELED ARE PRESENT IN CRYO/CRYSTALLIZATION CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.183 3709 5 %RANDOM
Rwork0.15 ---
all0.152 ---
obs0.152 73782 99.28 %-
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
1-1.35 Å20 Å20 Å2
2---0.98 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4327 0 41 621 4989
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224667
X-RAY DIFFRACTIONr_bond_other_d0.0010.023137
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.9636366
X-RAY DIFFRACTIONr_angle_other_deg0.92537748
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5515630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.18324.772197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.50715814
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.3921522
X-RAY DIFFRACTIONr_chiral_restr0.0890.2737
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025233
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02889
X-RAY DIFFRACTIONr_nbd_refined0.2190.2977
X-RAY DIFFRACTIONr_nbd_other0.1840.23275
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22323
X-RAY DIFFRACTIONr_nbtor_other0.0870.22382
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2467
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2820.297
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.235
X-RAY DIFFRACTIONr_mcbond_it1.97433003
X-RAY DIFFRACTIONr_mcbond_other0.61731198
X-RAY DIFFRACTIONr_mcangle_it3.00854743
X-RAY DIFFRACTIONr_scbond_it4.8781865
X-RAY DIFFRACTIONr_scangle_it6.791111590
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1609MEDIUM POSITIONAL0.210.5
1864LOOSE POSITIONAL0.575
1609MEDIUM THERMAL0.972
1864LOOSE THERMAL2.1210
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 267 -
Rwork0.193 5079 -
obs-5346 98.76 %

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