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- PDB-1vk6: Crystal structure of NADH pyrophosphatase (1790429) from Escheric... -

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Entry
Database: PDB / ID: 1vk6
TitleCrystal structure of NADH pyrophosphatase (1790429) from Escherichia coli k12 at 2.20 A resolution
ComponentsNADH pyrophosphatase
KeywordsHYDROLASE / 1790429 / NADH PYROPHOSPHATASE / STRUCTURAL GENOMICS / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics
Function / homology
Function and homology information


: / NADP catabolic process / NAD+ diphosphatase / NAD+ diphosphatase activity / NADH pyrophosphatase activity / RNA NAD-cap (NMN-forming) hydrolase activity / NAD-cap decapping / NAD catabolic process / mRNA stabilization / NADH metabolic process ...: / NADP catabolic process / NAD+ diphosphatase / NAD+ diphosphatase activity / NADH pyrophosphatase activity / RNA NAD-cap (NMN-forming) hydrolase activity / NAD-cap decapping / NAD catabolic process / mRNA stabilization / NADH metabolic process / mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / peroxisome / manganese ion binding / magnesium ion binding / protein homodimerization activity / zinc ion binding / cytosol
Similarity search - Function
Nucleoside Triphosphate Pyrophosphohydrolase - #20 / : / NAD-capped RNA hydrolase NudC / Zinc ribbon, NADH pyrophosphatase / NADH pyrophosphatase zinc ribbon domain / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain ...Nucleoside Triphosphate Pyrophosphohydrolase - #20 / : / NAD-capped RNA hydrolase NudC / Zinc ribbon, NADH pyrophosphatase / NADH pyrophosphatase zinc ribbon domain / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
NAD-capped RNA hydrolase NudC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of NADH pyrophosphatase (1790429) from Escherichia coli k12 at 2.20 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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
Remark 999 SEQUENCE CLONING ARTIFACT: THE CONSTRUCT WAS PCR AMPLIFIED WITH TAQ POLYMERASE. SEQUENCING OF THE ... SEQUENCE CLONING ARTIFACT: THE CONSTRUCT WAS PCR AMPLIFIED WITH TAQ POLYMERASE. SEQUENCING OF THE CLONED CONSTRUCT INDICATED THAT ARG IN POSITION 33 WAS MUTATED TO ALA. HOWEVER, THE LOCATION OF ALA33 WITHIN THE STRUCTURE SUGGESTS THAT A LARGE SIDE CHAIN AT THIS POSITION IS UNLIKELY WITHOUT SIGNIFICANT STRUCTURAL CHANGES.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADH pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9825
Polymers31,5621
Non-polymers4204
Water1,72996
1
A: NADH pyrophosphatase
hetero molecules

A: NADH pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,96310
Polymers63,1232
Non-polymers8408
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Buried area4900 Å2
ΔGint-95 kcal/mol
Surface area24270 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)127.319, 127.319, 108.405
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-310-

HOH

21A-322-

HOH

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Components

#1: Protein NADH pyrophosphatase


Mass: 31561.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: NUDC, B3996 / Production host: Escherichia coli (E. coli)
References: UniProt: P32664, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 4.13 Å3/Da / Density % sol: 69.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop
Details: 12% MPD, 0.08M HEPES, 0.02M HEPES_Na , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587
DetectorType: ADSC / Detector: CCD / Date: Oct 21, 2003
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.2→63.66 Å / Num. obs: 26842 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 53.64 Å2 / Rsym value: 0.068 / Net I/σ(I): 13.9
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 3836 / Rsym value: 0.588 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0001refinement
SCALA4.2)data scaling
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→63.66 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.866 / SU ML: 0.116 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE METAL SITE COORDINATED BY CYS98, CYS101, CYS116, CYS119 IS TENATIVELY ASSIGNED AS ZINC BASED ON SEQUENCE HOMOLOGY. IT IS CONSISTENT WITH ELECTRON DENSITY AND COORDINATION. OTHER METALS ...Details: THE METAL SITE COORDINATED BY CYS98, CYS101, CYS116, CYS119 IS TENATIVELY ASSIGNED AS ZINC BASED ON SEQUENCE HOMOLOGY. IT IS CONSISTENT WITH ELECTRON DENSITY AND COORDINATION. OTHER METALS SUCH AS IRON ARE ALSO POSSIBLE. ELECTRON DENSITY AT THE C-TERMINUS IS POOR.
RfactorNum. reflection% reflectionSelection details
Rfree0.21955 1371 5.1 %RANDOM
Rwork0.18668 ---
obs0.18831 25436 99.87 %-
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: 68.881 Å2
Baniso -1Baniso -2Baniso -3
1-1.85 Å20.92 Å20 Å2
2--1.85 Å20 Å2
3----2.77 Å2
Refinement stepCycle: LAST / Resolution: 2.2→63.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2053 0 25 96 2174
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212149
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.9362925
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8245256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7123.524105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.85115351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1351516
X-RAY DIFFRACTIONr_chiral_restr0.1020.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021646
X-RAY DIFFRACTIONr_nbd_refined0.1950.2890
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2113
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.215
X-RAY DIFFRACTIONr_mcbond_it2.45231324
X-RAY DIFFRACTIONr_mcangle_it3.46652074
X-RAY DIFFRACTIONr_scbond_it6.2518963
X-RAY DIFFRACTIONr_scangle_it7.92811851
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 113 5.85 %
Rwork0.25 1818 -
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)
11.69060.71421.2990.68091.3345.5790.0391-0.24510.03520.204-0.14110.00640.40560.29780.1021-0.1934-0.1513-0.0191-0.0250.0859-0.166682.03541.6178.911
22.21560.70161.60642.11591.21027.2225-0.37260.05640.7209-0.024-0.10530.2295-1.63160.22410.4780.1509-0.2671-0.1763-0.02640.12350.058893.34168.942-1.053
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
110 - 12712 - 139
22128 - 256140 - 268

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