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- PDB-3ztv: Structure of Haemophilus influenzae NAD nucleotidase (NadN) -

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Basic information

Entry
Database: PDB / ID: 3ztv
TitleStructure of Haemophilus influenzae NAD nucleotidase (NadN)
ComponentsNAD NUCLEOTIDASE
KeywordsHYDROLASE / NAD PYROPHOSPHATASE / NMN NUCLEOTIDASE / PERIPLASMIC ENZYME / CD73
Function / homology
Function and homology information


cellular anatomical entity / UDP-sugar diphosphatase activity / nucleotide catabolic process / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / outer membrane-bounded periplasmic space / nucleotide binding / metal ion binding
Similarity search - Function
NAD pyrophosphatase/5-nucleotidase NadN / 5'-nucleotidase; domain 2 / 5'-Nucleotidase, C-terminal 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 ...NAD pyrophosphatase/5-nucleotidase NadN / 5'-nucleotidase; domain 2 / 5'-Nucleotidase, C-terminal 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 Complex / Alpha Beta
Similarity search - Domain/homology
ADENOSINE / NAD 5'-nucleotidase / NAD nucleotidase
Similarity search - Component
Biological speciesHAEMOPHILUS INFLUENZAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsGaravaglia, S. / Bruzzone, S. / Cassani, C. / Canella, L. / Allegrone, G. / Sturla, L. / Mannino, E. / Millo, E. / De Flora, A. / Rizzi, M.
CitationJournal: Biochem.J. / Year: 2012
Title: The High-Resolution Crystal Structure of Periplasmic Haemophilus Influenzae Nad Nucleotidase Reveals a Novel Enzymatic Function of Human Cd73 Related to Nad Metabolism.
Authors: Garavaglia, S. / Bruzzone, S. / Cassani, C. / Canella, L. / Allegrone, G. / Sturla, L. / Mannino, E. / Millo, E. / De Flora, A. / Rizzi, M.
History
DepositionJul 12, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Other
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD NUCLEOTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2535
Polymers63,7631
Non-polymers4904
Water11,331629
1
A: NAD NUCLEOTIDASE
hetero molecules

A: NAD NUCLEOTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,50610
Polymers127,5262
Non-polymers9808
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area3220 Å2
ΔGint-167.3 kcal/mol
Surface area43390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.640, 126.607, 200.486
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2302-

HOH

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Components

#1: Protein NAD NUCLEOTIDASE / NADN


Mass: 63763.074 Da / Num. of mol.: 1 / Fragment: RESIDUES 25-603
Source method: isolated from a genetically manipulated source
Details: FRAGMENT CORRESPONDS TO MATURE PROTEIN / Source: (gene. exp.) HAEMOPHILUS INFLUENZAE (bacteria) / Strain: RD KW20 / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q4QNY4, UniProt: P44569*PLUS, 5'-nucleotidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 629 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST 26 RESIDUES CORRESPONDING TO THE SIGNAL PEPTIDE (PELB) WERE CLEAVED OFF IN THE ...THE FIRST 26 RESIDUES CORRESPONDING TO THE SIGNAL PEPTIDE (PELB) WERE CLEAVED OFF IN THE RECOMBINANT ENZYME CRYSTALLIZED.

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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: 2.72 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 6.5 / Details: 25% P/V PEG 1500, 0.1 M MES, PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.3→20 Å / Num. obs: 166343 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 8.86 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.1
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.1 / % possible all: 94

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Z1A

2z1a


Resolution: 1.3→31.687 Å / SU ML: 0.16 / σ(F): 1.13 / Phase error: 22.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2342 1479 0.5 %
Rwork0.2003 --
obs0.2005 162525 94.9 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.813 Å2 / ksol: 0.368 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.8311 Å20 Å20 Å2
2--3.9137 Å20 Å2
3----2.0826 Å2
Refinement stepCycle: LAST / Resolution: 1.3→31.687 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4391 0 27 629 5047
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064510
X-RAY DIFFRACTIONf_angle_d1.0666104
X-RAY DIFFRACTIONf_dihedral_angle_d12.0651658
X-RAY DIFFRACTIONf_chiral_restr0.076677
X-RAY DIFFRACTIONf_plane_restr0.005786
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.34650.2641540.274628591X-RAY DIFFRACTION87
1.3465-1.40040.24741450.234330036X-RAY DIFFRACTION91
1.4004-1.46410.21541560.218330653X-RAY DIFFRACTION93
1.4641-1.54130.21831020.201631082X-RAY DIFFRACTION94
1.5413-1.63790.20091620.188231384X-RAY DIFFRACTION95
1.6379-1.76430.23421340.189131734X-RAY DIFFRACTION96
1.7643-1.94180.30281480.218831860X-RAY DIFFRACTION97
1.9418-2.22280.22261360.188532404X-RAY DIFFRACTION98
2.2228-2.80020.24061630.202432533X-RAY DIFFRACTION99
2.8002-31.69660.22061790.185231858X-RAY DIFFRACTION97

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