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- PDB-2gb5: Crystal structure of NADH pyrophosphatase (EC 3.6.1.22) (1790429)... -

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Basic information

Entry
Database: PDB / ID: 2gb5
TitleCrystal structure of NADH pyrophosphatase (EC 3.6.1.22) (1790429) from Escherichia coli K12 at 2.30 A resolution
ComponentsNADH pyrophosphatase
KeywordsHYDROLASE / 1790429 / NADH pyrophosphatase (EC 3.6.1.22) / Structural Genomics / PSI / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG
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 / manganese ion binding / magnesium ion binding / protein homodimerization activity / zinc ion binding
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 / MAD / Resolution: 2.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of NADH pyrophosphatase (EC 3.6.1.22) (1790429) from Escherichia coli K12 at 2.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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_conn.ptnr2_label_seq_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 999SEQUENCE 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

Downloads & links

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Assembly

Deposited unit
A: NADH pyrophosphatase
B: NADH pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3484
Polymers63,2172
Non-polymers1312
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-13 kcal/mol
Surface area24340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.287, 103.553, 57.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg label comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISGLU4AA-3 - 2469 - 258
21HISGLU4BB-3 - 2469 - 258
32ASPTYR6AA247 - 256259 - 268
42ASPTYR6BB247 - 256259 - 268

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Components

#1: Protein NADH pyrophosphatase


Mass: 31608.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: nudC / Production host: Escherichia coli (E. coli) / References: UniProt: P32664, NAD+ diphosphatase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.36 Å3/Da / Density % sol: 47.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop
Details: 9.975% PEG MME 5000, 0.05M Acetic Acid, 0.052M Citrate_Na3, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9802, 1.0000
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 18, 2003
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.98021
211
ReflectionResolution: 2.3→49.629 Å / Num. obs: 26695 / % possible obs: 99.1 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 5.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRsym value% possible all
2.3-2.362.70.3842487017730.38491.6
2.36-2.423.20.3712595018770.37198.5
2.42-2.493.50.3362.3660518740.336100
2.49-2.573.60.2722.8638517970.272100
2.57-2.663.50.2273.3624817630.227100
2.66-2.753.60.1784.1604717010.178100
2.75-2.853.50.1455.1576116290.145100
2.85-2.973.50.126561715910.12100
2.97-3.13.50.0977.1533615140.097100
3.1-3.253.50.0897.6510314520.08999.9
3.25-3.433.50.0778.8488813990.07799.8
3.43-3.643.50.0689.5455513100.06899.8
3.64-3.893.40.0653.7423312420.065100
3.89-4.23.40.0513401511710.05100
4.2-4.63.40.04713.4363010740.04799.8
4.6-5.143.30.05111.532769890.05199.8
5.14-5.943.10.05810.627058680.05899.7
5.94-7.272.90.0698.721807400.06999
7.27-10.293.40.04612.219895880.04699.2
10.29-49.633.10.04314.810473430.04396.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→49.61 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.917 / SU B: 15.341 / SU ML: 0.201 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.358 / ESU R Free: 0.248
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1345 5 %RANDOM
Rwork0.198 ---
all0.201 ---
obs-26666 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.389 Å2
Baniso -1Baniso -2Baniso -3
1--3.03 Å20 Å20 Å2
2--2.14 Å20 Å2
3---0.89 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4171 0 2 240 4413
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0214338
X-RAY DIFFRACTIONr_bond_other_d0.0010.023845
X-RAY DIFFRACTIONr_angle_refined_deg1.2251.9355911
X-RAY DIFFRACTIONr_angle_other_deg0.76838896
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2255534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.1123.524210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.45515689
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1181531
X-RAY DIFFRACTIONr_chiral_restr0.0690.2625
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024899
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02907
X-RAY DIFFRACTIONr_nbd_refined0.170.2804
X-RAY DIFFRACTIONr_nbd_other0.1750.23957
X-RAY DIFFRACTIONr_nbtor_refined0.1710.22065
X-RAY DIFFRACTIONr_nbtor_other0.0820.22555
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2215
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1110.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1540.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.25
X-RAY DIFFRACTIONr_mcbond_it1.59932712
X-RAY DIFFRACTIONr_mcbond_other0.37731073
X-RAY DIFFRACTIONr_mcangle_it2.08154254
X-RAY DIFFRACTIONr_scbond_it3.81981894
X-RAY DIFFRACTIONr_scangle_it5.296111656
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
3643MEDIUM POSITIONAL0.40.5
123LOOSE POSITIONAL0.875
3643MEDIUM THERMAL0.652
123LOOSE THERMAL3.310
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 87 -
Rwork0.24 1683 -
obs-1770 91.14 %
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)
12.9184-0.9115-0.50421.60830.15193.60620.03340.12920.56610.0230.02290.0401-0.3334-0.1526-0.0563-0.1465-0.02140.018-0.17050.00980.049-29.80612.7988.2976
20.1811-0.259-0.72910.72750.82873.06460.01970.1098-0.00370.078-0.0154-0.03950.0307-0.0113-0.0043-0.0421-0.0352-0.01450.06150.0105-0.037-27.1858-10.555137.5332
32.8052-0.24220.06695.511-0.97981.72110.1133-0.1727-0.22890.2116-0.2103-0.28550.21230.43110.097-0.11670.0283-0.03440.10390.031-0.1023-4.4779-18.519417.0769
43.30571.1953-0.03441.11760.473.175-0.0966-0.1248-0.5760.02580.05970.04280.7194-0.40410.03680.0877-0.10450.00710.02220.00320.088-35.2552-26.832413.7802
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA-7 - 1275 - 139
22AA128 - 257140 - 269
33BB-4 - 1278 - 139
44BB128 - 256140 - 268

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