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- PDB-4gik: Crystal Structure of Pseudouridine Monophosphate Glycosidase/Line... -

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Basic information

Entry
Database: PDB / ID: 4gik
TitleCrystal Structure of Pseudouridine Monophosphate Glycosidase/Linear R5P Adduct
ComponentsPseudouridine-5'-phosphate glycosidase
KeywordsHYDROLASE / alpha-beta-alpha sandwich fold
Function / homology
Function and homology information


nucleobase catabolic process / pseudouridylate synthase / pseudouridylate synthase activity / hydrolase activity, acting on glycosyl bonds / manganese ion binding / protein-containing complex / identical protein binding / cytoplasm
Similarity search - Function
Indigoidine synthase fold / Indigoidine synthase domain / Pseudouridine-5'-phosphate glycosidase / Indigoidine synthase A-like / Indigoidine synthase A like protein / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / RIBOSE-5-PHOSPHATE / Pseudouridine-5'-phosphate glycosidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.187 Å
AuthorsHuang, S. / Mahanta, N. / Begley, T.P. / Ealick, S.E.
CitationJournal: Biochemistry / Year: 2012
Title: Pseudouridine monophosphate glycosidase: a new glycosidase mechanism.
Authors: Huang, S. / Mahanta, N. / Begley, T.P. / Ealick, S.E.
History
DepositionAug 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pseudouridine-5'-phosphate glycosidase
B: Pseudouridine-5'-phosphate glycosidase
C: Pseudouridine-5'-phosphate glycosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,7269
Polymers106,8713
Non-polymers8556
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8840 Å2
ΔGint-77 kcal/mol
Surface area30860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.347, 116.496, 132.153
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Pseudouridine-5'-phosphate glycosidase / pseudouridine monophosphate glycosidase / PsiMP glycosidase


Mass: 35623.652 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: b2165, JW2152, psuG, yeiN / Plasmid: THT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P33025, Hydrolases; Glycosylases
#2: Sugar ChemComp-R5P / RIBOSE-5-PHOSPHATE


Type: saccharide / Mass: 230.110 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C5H11O8P
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.21 Å3/Da / Density % sol: 44.33 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 22% PEG4000, 0.1 M Tris, 0.2 M sodium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 8, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.187→50 Å / Num. all: 49764 / Num. obs: 49152 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 7.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.187-2.2840.47199.9
2.28-2.374.10.375199.9
2.37-2.484.10.3181100
2.48-2.614.10.2391100
2.61-2.7740.1781100
2.77-2.9940.1321100
2.99-3.2940.099199.9
3.29-3.7640.073199.9
3.76-4.743.90.049199.6
4.74-503.80.03198.9

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VKM

1vkm


Resolution: 2.187→41.204 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.6 / σ(F): 1.36 / Phase error: 24.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2313 2532 5.15 %
Rwork0.1792 --
obs0.1819 49141 98.73 %
all-49764 -
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.404 Å2 / ksol: 0.321 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-13.1086 Å2-0 Å2-0 Å2
2---8.4708 Å20 Å2
3----4.6379 Å2
Refinement stepCycle: LAST / Resolution: 2.187→41.204 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6555 0 42 322 6919
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076711
X-RAY DIFFRACTIONf_angle_d1.1789146
X-RAY DIFFRACTIONf_dihedral_angle_d13.1342350
X-RAY DIFFRACTIONf_chiral_restr0.0741139
X-RAY DIFFRACTIONf_plane_restr0.0061179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1867-2.22880.33021070.22822064X-RAY DIFFRACTION80
2.2288-2.27430.30831360.21092627X-RAY DIFFRACTION100
2.2743-2.32370.2581560.20342538X-RAY DIFFRACTION100
2.3237-2.37780.28281410.20212574X-RAY DIFFRACTION100
2.3778-2.43720.27651450.22062587X-RAY DIFFRACTION100
2.4372-2.50310.28271260.22262593X-RAY DIFFRACTION100
2.5031-2.57670.29121540.2052597X-RAY DIFFRACTION100
2.5767-2.65990.28211360.20482615X-RAY DIFFRACTION100
2.6599-2.7550.27451470.1922587X-RAY DIFFRACTION100
2.755-2.86520.25461510.19252599X-RAY DIFFRACTION100
2.8652-2.99560.2641260.192604X-RAY DIFFRACTION100
2.9956-3.15350.24261280.18822639X-RAY DIFFRACTION100
3.1535-3.3510.27511550.18782599X-RAY DIFFRACTION100
3.351-3.60960.25081160.18692673X-RAY DIFFRACTION100
3.6096-3.97250.1841590.15972612X-RAY DIFFRACTION100
3.9725-4.54670.19021540.13972651X-RAY DIFFRACTION100
4.5467-5.7260.19661530.15012655X-RAY DIFFRACTION99
5.726-41.21090.17931420.17362795X-RAY DIFFRACTION99
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)
11.16961.06090.3865.3644-1.02531.8133-0.05220.1215-0.1257-0.7527-0.02060.06550.0872-0.19960.0760.1870.0121-0.04760.2591-0.01310.221315.4118-19.4345-23.9739
20.95120.21980.52852.14720.0831.46990.03940.1707-0.1602-0.2283-0.0035-0.1342-0.03010.2450.00490.0830.01560.0110.1894-0.0060.157829.4661-19.6311-12.5667
30.27410.41280.29121.07240.08610.5824-0.1032-0.4821-0.00540.3633-0.23230.8997-0.0174-0.61380.12610.2388-0.00340.15060.4071-0.11110.425611.9569-7.171120.1385
42.5813-0.7560.09583.96821.58864.50720.1224-0.34230.08990.64380.4581-0.57710.63870.7903-0.5310.46770.1009-0.03730.482-0.09140.300630.2462-7.490225.9609
50.9348-0.0682-0.50542.60941.77913.3711-0.2207-0.246-0.19560.86310.15510.02160.69340.22890.09390.34940.08720.07390.30870.03920.261924.6964-14.257419.0265
60.6076-0.33970.31862.5830.45721.9998-0.0778-0.06050.01980.01710.00870.0742-0.18570.04150.06770.1028-0.00590.00290.1742-0.0240.150528.1994-6.9157.9433
71.47110.0819-0.36232.9530.75433.2245-0.029-0.16210.2750.00030.0775-0.1225-0.71160.2844-0.03070.3061-0.0541-0.03940.1936-0.01120.174231.17598.241410.2065
86.44380.09693.30193.7240.20726.4371-0.0112-0.23580.4040.1177-0.0113-0.2765-0.23120.3665-0.02670.2462-0.05920.06930.2825-0.03750.176532.61646.908316.2938
93.34071.43781.00722.39080.54012.6902-0.0679-0.28990.03290.18860.1707-0.5707-0.03010.6824-0.10350.17170.0177-0.05360.4678-0.06790.333247.9601-8.155313.3887
108.4967-2.2070.57414.30880.24464.0296-0.0425-0.77070.2170.37440.1422-0.0798-0.17740.0016-0.08250.27420.0160.00590.2256-0.01970.135328.03784.165122.9428
110.7099-0.93030.58491.4388-0.63792.166-0.24020.14330.2788-0.5874-0.07240.2473-1.3224-0.10770.20861.03080.1721-0.30110.16160.02210.3917.171422.8694-7.8541
120.5007-0.09870.43440.62310.09521.5389-0.22670.32840.3913-0.49090.1163-0.0822-1.03460.34180.12680.7743-0.1574-0.07870.01040.269-0.010428.502512.58-19.0524
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 6:104)
2X-RAY DIFFRACTION2chain 'A' and (resseq 105:311)
3X-RAY DIFFRACTION3chain 'B' and (resseq 5:30)
4X-RAY DIFFRACTION4chain 'B' and (resseq 31:58)
5X-RAY DIFFRACTION5chain 'B' and (resseq 59:98)
6X-RAY DIFFRACTION6chain 'B' and (resseq 99:155)
7X-RAY DIFFRACTION7chain 'B' and (resseq 156:224)
8X-RAY DIFFRACTION8chain 'B' and (resseq 225:244)
9X-RAY DIFFRACTION9chain 'B' and (resseq 245:283)
10X-RAY DIFFRACTION10chain 'B' and (resseq 284:311)
11X-RAY DIFFRACTION11chain 'C' and (resseq 6:123)
12X-RAY DIFFRACTION12chain 'C' and (resseq 124:311)

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