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- PDB-5eqv: 1.45 Angstrom Crystal Structure of Bifunctional 2',3'-cyclic Nucl... -

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Basic information

Entry
Database: PDB / ID: 5eqv
Title1.45 Angstrom Crystal Structure of Bifunctional 2',3'-cyclic Nucleotide 2'-phosphodiesterase/3'-Nucleotidase Periplasmic Precursor Protein from Yersinia pestis with Phosphate bound to the Active site
Componentsbifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase periplasmic precursor protein
KeywordsHYDROLASE / bifunctional 2' / 3'-cyclic nucleotide / 2'-phosphodiesterase/3'-nucleotidase / periplasmic precursor protein / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


2',3'-cyclic-nucleotide 2'-phosphodiesterase / 2',3'-cyclic-nucleotide 2'-phosphodiesterase activity / nucleotidase activity / nucleotide catabolic process / cell envelope / nucleotide binding / metal ion binding
Similarity search - Function
2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase / CpdB, N-terminal metallophosphatase domain / 5'-nucleotidase signature 1. / 5'-Nucleotidase, conserved site / 5'-nucleotidase signature 2. / 5'-Nucleotidase, C-terminal / 5'-nucleotidase, C-terminal domain / 5'-Nucleotidase/apyrase / 5'-Nucleotidase, C-terminal domain superfamily / Metallo-dependent phosphatases ...2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase / CpdB, N-terminal metallophosphatase domain / 5'-nucleotidase signature 1. / 5'-Nucleotidase, conserved site / 5'-nucleotidase signature 2. / 5'-Nucleotidase, C-terminal / 5'-nucleotidase, C-terminal domain / 5'-Nucleotidase/apyrase / 5'-Nucleotidase, C-terminal domain superfamily / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / D-MALATE / TRIETHYLENE GLYCOL / PHOSPHATE ION / : / 2',3'-cyclic-nucleotide 2'-phosphodiesterase
Similarity search - Component
Biological speciesYersinia pestis CO92 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsMinasov, G. / Shuvalova, L. / Brunzelle, J.S. / Kiryukhina, O. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 1.45 Angstrom Crystal Structure of Bifunctional 2',3'-cyclic Nucleotide 2'-phosphodiesterase/3'-Nucleotidase Periplasmic Precursor Protein from Yersinia pestis with Phosphate bound to the Active site.
Authors: Minasov, G. / Shuvalova, L. / Brunzelle, J.S. / Kiryukhina, O. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase periplasmic precursor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7979
Polymers37,1381
Non-polymers6598
Water11,331629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.282, 107.282, 63.357
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-760-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase periplasmic precursor protein


Mass: 37137.914 Da / Num. of mol.: 1 / Fragment: UNP residues 22-358
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis CO92 (bacteria) / Gene: cpdB, AK38_3205 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0B6NVJ4, UniProt: A0A0H2W1T3*PLUS, 2',3'-cyclic-nucleotide 2'-phosphodiesterase

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Non-polymers , 7 types, 637 molecules

#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 629 / 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: 2.38 Å3/Da / Density % sol: 48.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein: 8.6 mg/ml, 0.01M Tris-HCL (pH 8.3), 5mM Thymidine; Screen: Classics II (F11), 0.2M Sodium chloride, 0.1M Bis-Tris (pH 6.5), 25% (w/v) PEG 3350;

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 19, 2015
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. obs: 65853 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 12.6 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 42.6
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 5.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
BLU-MAXdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB3JYF

Resolution: 1.45→29.91 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.679 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15302 3280 5 %RANDOM
Rwork0.13195 ---
obs0.13301 62495 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.268 Å2
Baniso -1Baniso -2Baniso -3
1--1.07 Å20 Å20 Å2
2---1.07 Å20 Å2
3---2.13 Å2
Refinement stepCycle: 1 / Resolution: 1.45→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2592 0 36 629 3257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192881
X-RAY DIFFRACTIONr_bond_other_d0.0020.022738
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.9633942
X-RAY DIFFRACTIONr_angle_other_deg0.91336335
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2055379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.57525.591127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.69115483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.022159
X-RAY DIFFRACTIONr_chiral_restr0.1050.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.0213403
X-RAY DIFFRACTIONr_gen_planes_other0.0190.02640
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9461.321454
X-RAY DIFFRACTIONr_mcbond_other0.9391.3171452
X-RAY DIFFRACTIONr_mcangle_it1.4751.9771853
X-RAY DIFFRACTIONr_mcangle_other1.4771.9781854
X-RAY DIFFRACTIONr_scbond_it1.5621.5571427
X-RAY DIFFRACTIONr_scbond_other1.5561.5571427
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4492.2422090
X-RAY DIFFRACTIONr_long_range_B_refined7.1113926
X-RAY DIFFRACTIONr_long_range_B_other6.2293414
X-RAY DIFFRACTIONr_rigid_bond_restr4.58534
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded9.50257
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.191 237 -
Rwork0.173 4519 -
obs--99.77 %
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)
10.81150.1856-0.08450.6823-0.16550.9751-0.00970.08430.0703-0.07960.03460.0111-0.0148-0.0302-0.02490.0292-0.0040.00530.02110.00880.008-4.747825.29399.4529
20.64980.2891-0.08860.6214-0.08350.35160.0042-0.0278-0.02250.0211-0.0191-0.0753-0.00480.02430.01490.01790.00330.00140.0230.00620.0116.397228.810621.2848
30.9950.08130.02160.77290.28220.49950.0130.106-0.0061-0.10520.0080.02020.06790.0143-0.0210.0557-0.0060.00530.05480.0050.0357-5.766120.206310.5898
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 104
2X-RAY DIFFRACTION2A105 - 312
3X-RAY DIFFRACTION3A313 - 362

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