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- PDB-4n7t: Crystal structure of phosphorylated phosphopentomutase from strep... -

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Basic information

Entry
Database: PDB / ID: 4n7t
TitleCrystal structure of phosphorylated phosphopentomutase from streptococcus mutans
ComponentsPhosphopentomutase
KeywordsISOMERASE / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / New York Structural Genomics Research Consortium / NYSGXRC / NYSGRC / PHOSPHORYLATED PHOSPHOPENTOMUTASE / MANGANESE Binding / Phosphorylated THR 92 in the active site
Function / homology
Function and homology information


phosphopentomutase / phosphopentomutase activity / cellular metabolic compound salvage / 2-deoxyribose 1-phosphate catabolic process / 5-phosphoribose 1-diphosphate biosynthetic process / nucleotide metabolic process / manganese ion binding / magnesium ion binding / cytoplasm
Similarity search - Function
Phosphopentomutase / Phosphopentomutase / Phosphopentomutase DeoB cap domain superfamily / Metalloenzyme / Metalloenzyme superfamily / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich ...Phosphopentomutase / Phosphopentomutase / Phosphopentomutase DeoB cap domain superfamily / Metalloenzyme / Metalloenzyme superfamily / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
AZIDE ION / : / DI(HYDROXYETHYL)ETHER / Phosphopentomutase
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.996 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Bonanno, J. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of phosphorylated phosphopentomutase from streptococcus mutans
Authors: Fedorov, A.A. / Fedorov, E.V. / Bonanno, J. / Burley, S.K. / Almo, S.C.
History
DepositionOct 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Structure summary
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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_auth_seq_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 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphopentomutase
B: Phosphopentomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,47814
Polymers90,5992
Non-polymers87812
Water6,503361
1
A: Phosphopentomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9309
Polymers45,3001
Non-polymers6308
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphopentomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5485
Polymers45,3001
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.788, 63.687, 104.765
Angle α, β, γ (deg.)90.00, 98.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Phosphopentomutase / Phosphodeoxyribomutase


Mass: 45299.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: ATCC 700610 / UA159 / Gene: deoB, SMU_1233 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DTU0, phosphopentomutase

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Non-polymers , 6 types, 373 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 2.54 Å3/Da / Density % sol: 51.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 19% PEG 3350, 0.1M BIS-TRIS, 0.2M LITHIUM SULFATE, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 6, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.996→29.268 Å / Num. all: 61424 / Num. obs: 61424 / % possible obs: 99.13 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3M7V

3m7v


Resolution: 1.996→29.268 Å / SU ML: 0.21 / σ(F): 0 / Phase error: 20.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2025 1871 3.05 %RANDOM
Rwork0.1706 ---
all0.1716 61424 --
obs0.1716 61424 99.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.996→29.268 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6182 0 45 361 6588
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076359
X-RAY DIFFRACTIONf_angle_d1.048646
X-RAY DIFFRACTIONf_dihedral_angle_d11.8972298
X-RAY DIFFRACTIONf_chiral_restr0.073969
X-RAY DIFFRACTIONf_plane_restr0.0051131
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9964-2.05040.2541640.19344406X-RAY DIFFRACTION96
2.0504-2.11070.27251380.17654520X-RAY DIFFRACTION99
2.1107-2.17880.21721300.17394584X-RAY DIFFRACTION99
2.1788-2.25660.20721340.17854593X-RAY DIFFRACTION99
2.2566-2.34690.23071230.17934555X-RAY DIFFRACTION99
2.3469-2.45370.25511350.18024595X-RAY DIFFRACTION100
2.4537-2.5830.22631310.18454595X-RAY DIFFRACTION100
2.583-2.74470.20711420.18764615X-RAY DIFFRACTION100
2.7447-2.95640.23561480.18684597X-RAY DIFFRACTION100
2.9564-3.25360.21421470.18374620X-RAY DIFFRACTION100
3.2536-3.72360.19971660.1744623X-RAY DIFFRACTION100
3.7236-4.68820.16681470.14484613X-RAY DIFFRACTION99
4.6882-29.27120.17121660.15444637X-RAY DIFFRACTION98
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)
11.5529-0.0272-0.1590.7529-0.10571.41370.0504-0.09690.36810.02960.0282-0.0301-0.25210.0557-0.0520.1660.00990.00930.17880.00110.198513.524531.506318.933
22.27990.1212-0.52410.8443-0.30721.25280.0053-0.0537-0.01060.1979-0.045-0.0357-0.04140.02880.03090.18430.0072-0.02790.13640.05480.14546.05915.300433.2624
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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