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- PDB-4hao: Crystal Structure of Inorganic Polyphosphate/ATP-NAD Kinase from ... -

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Basic information

Entry
Database: PDB / ID: 4hao
TitleCrystal Structure of Inorganic Polyphosphate/ATP-NAD Kinase from Yersinia pestis CO92
ComponentsProbable inorganic polyphosphate/ATP-NAD kinase
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / beta-fold / SBP fold / kinase
Function / homology
Function and homology information


NAD+ kinase / NAD+ kinase activity / NADP biosynthetic process / NAD metabolic process / NAD binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Probable inorganic polyphosphate/atp-NAD kinase; domain 1 / Probable inorganic polyphosphate/atp-NAD kinase; domain 2 / ATP-NAD kinase C-terminal domain / NAD kinase / ATP-NAD kinase, PpnK-type, C-terminal / ATP-NAD kinase N-terminal domain / NAD kinase/diacylglycerol kinase-like domain superfamily / Inorganic polyphosphate/ATP-NAD kinase, N-terminal / Tumour Suppressor Smad4 / Sandwich ...Probable inorganic polyphosphate/atp-NAD kinase; domain 1 / Probable inorganic polyphosphate/atp-NAD kinase; domain 2 / ATP-NAD kinase C-terminal domain / NAD kinase / ATP-NAD kinase, PpnK-type, C-terminal / ATP-NAD kinase N-terminal domain / NAD kinase/diacylglycerol kinase-like domain superfamily / Inorganic polyphosphate/ATP-NAD kinase, N-terminal / Tumour Suppressor Smad4 / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / NAD kinase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.551 Å
AuthorsKim, Y. / Maltseva, N. / Jedrzejczak, R. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Inorganic Polyphosphate/ATP-NAD Kinase from Yersinia pestis CO92
Authors: Kim, Y. / Maltseva, N. / Jedrzejczak, R. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_ref_seq_dif.details / _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: Probable inorganic polyphosphate/ATP-NAD kinase
B: Probable inorganic polyphosphate/ATP-NAD kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,71615
Polymers67,8632
Non-polymers85313
Water86548
1
A: Probable inorganic polyphosphate/ATP-NAD kinase
hetero molecules

A: Probable inorganic polyphosphate/ATP-NAD kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,41610
Polymers67,8632
Non-polymers5528
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4090 Å2
ΔGint-66 kcal/mol
Surface area23990 Å2
MethodPISA
2
B: Probable inorganic polyphosphate/ATP-NAD kinase
hetero molecules

B: Probable inorganic polyphosphate/ATP-NAD kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,01620
Polymers67,8632
Non-polymers1,15318
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4030 Å2
ΔGint-68 kcal/mol
Surface area24700 Å2
MethodPISA
3
A: Probable inorganic polyphosphate/ATP-NAD kinase
hetero molecules

A: Probable inorganic polyphosphate/ATP-NAD kinase
hetero molecules

B: Probable inorganic polyphosphate/ATP-NAD kinase
hetero molecules

B: Probable inorganic polyphosphate/ATP-NAD kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,43230
Polymers135,7264
Non-polymers1,70526
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation2_565-x,y+1,-z1
Buried area12020 Å2
ΔGint-167 kcal/mol
Surface area44790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.091, 65.160, 86.386
Angle α, β, γ (deg.)90.00, 124.95, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-527-

HOH

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Components

#1: Protein Probable inorganic polyphosphate/ATP-NAD kinase / Poly(P)/ATP NAD kinase


Mass: 33931.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: un-cleavable C-terminal six-His tag / Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: ppnK, y3074, YPO1106, YP_1050 / Plasmid: pMCSG26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q8ZH09, NAD+ kinase
#2: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.35 Å3/Da / Density % sol: 47.59 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M sodium acetate trihydrate pH 4.6, 1 M magnesium sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 7, 2012 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 20436 / Num. obs: 20436 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 72.1 Å2 / Rsym value: 0.057 / Net I/σ(I): 16.5
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 1006 / Rsym value: 0.677 / % possible all: 98.6

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: dev_1032)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 2AN1

2an1


Resolution: 2.551→33.747 Å / SU ML: 0.34 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 30.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1046 5.13 %random
Rwork0.185 ---
all0.188 20378 --
obs0.188 20378 98.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.2 Å2
Refinement stepCycle: LAST / Resolution: 2.551→33.747 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4397 0 54 48 4499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084586
X-RAY DIFFRACTIONf_angle_d1.1226226
X-RAY DIFFRACTIONf_dihedral_angle_d15.2871647
X-RAY DIFFRACTIONf_chiral_restr0.076722
X-RAY DIFFRACTIONf_plane_restr0.005807
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.5512-2.68560.33961340.27112621275595
2.6856-2.85380.32761510.243627972948100
2.8538-3.0740.28491400.237927912931100
3.074-3.38310.28381340.205927882922100
3.3831-3.8720.26731520.194827922944100
3.872-4.8760.23331640.156927832947100
4.876-33.74950.2041710.17172760293196
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)
15.81042.05180.88991.42430.92268.21-0.0481-0.3918-0.51230.1146-0.00210.24960.02370.10320.06950.35430.13120.01230.40950.13680.611926.4343-4.439517.2215
25.2789-0.84240.39333.7005-0.98335.3034-0.13770.5754-0.3487-0.34320.1314-0.55740.11650.3540.00950.2196-0.07840.02460.3868-0.16970.47810.39166.5043-8.807
33.7091-0.1412-1.4061.4885-1.30295.0741-0.1622-0.1251-0.7984-0.051-0.0211-0.2456-0.01730.50530.22810.314-0.0269-0.03480.3509-0.08780.609412.76672.72643.5044
46.24061.0769-0.36134.04383.45435.68030.43891.13310.4994-0.5049-0.0196-0.4528-0.51530.731-0.43150.6885-0.06590.04180.86310.20240.425111.8448-21.2811-36.3802
53.9725-1.44612.55453.1051-3.17688.0770.16610.20690.2782-0.26470.28820.0251-0.4031-0.2939-0.43210.4672-0.06930.17740.4435-0.04060.386110.5826-25.7661-16.0483
63.9779-0.4398-0.44952.7904-0.66372.8320.06960.05430.34560.02990.1085-0.2399-0.2920.3673-0.11150.3333-0.08420.0550.3064-0.09650.26379.2012-32.2186-4.4367
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4:123 )
2X-RAY DIFFRACTION2chain 'A' and (resid 124:239 )
3X-RAY DIFFRACTION3chain 'A' and (resid 240:292 )
4X-RAY DIFFRACTION4chain 'B' and (resid 4:56 )
5X-RAY DIFFRACTION5chain 'B' and (resid 57:168 )
6X-RAY DIFFRACTION6chain 'B' and (resid 169:292 )

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