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- PDB-3nl9: Crystal structure of a putative NTP pyrophosphohydrolase (Exig_10... -

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Basic information

Entry
Database: PDB / ID: 3nl9
TitleCrystal structure of a putative NTP pyrophosphohydrolase (Exig_1061) from EXIGUOBACTERIUM SP. 255-15 at 1.78 A resolution
Componentsputative NTP pyrophosphohydrolase
KeywordsHYDROLASE / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyputative ntp pyrophosphohydrolase like fold / putative ntp pyrophosphohydrolase like domain / NTP pyrophosphohydrolase-like domain superfamily / Phosphoribosyl-ATP pyrophosphohydrolase-like / Phosphoribosyl-ATP pyrophosphohydrolase / Orthogonal Bundle / Mainly Alpha / Uncharacterized protein
Function and homology information
Biological speciesExiguobacterium sibiricum 255-15 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.78 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Structure of a putative NTP pyrophosphohydrolase: YP_001813558.1 from Exiguobacterium sibiricum 255-15.
Authors: Han, G.W. / Elsliger, M.A. / Yeates, T.O. / Xu, Q. / Murzin, A.G. / Krishna, S.S. / Jaroszewski, L. / Abdubek, P. / Astakhova, T. / Axelrod, H.L. / Carlton, D. / Chen, C. / Chiu, H.J. / ...Authors: Han, G.W. / Elsliger, M.A. / Yeates, T.O. / Xu, Q. / Murzin, A.G. / Krishna, S.S. / Jaroszewski, L. / Abdubek, P. / Astakhova, T. / Axelrod, H.L. / Carlton, D. / Chen, C. / Chiu, H.J. / Clayton, T. / Das, D. / Deller, M.C. / Duan, L. / Ernst, D. / Feuerhelm, J. / Grant, J.C. / Grzechnik, A. / Jin, K.K. / Johnson, H.A. / Klock, H.E. / Knuth, M.W. / Kozbial, P. / Kumar, A. / Lam, W.W. / Marciano, D. / McMullan, D. / Miller, M.D. / Morse, A.T. / Nigoghossian, E. / Okach, L. / Reyes, R. / Rife, C.L. / Sefcovic, N. / Tien, H.J. / Trame, C.B. / van den Bedem, H. / Weekes, D. / Hodgson, K.O. / Wooley, J. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionJun 21, 2010Deposition site: RCSB / Processing site: RCSB
SupersessionJul 21, 2010ID: 3MQU
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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: putative NTP pyrophosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5213
Polymers19,3971
Non-polymers1242
Water2,540141
1
A: putative NTP pyrophosphohydrolase
hetero molecules

A: putative NTP pyrophosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0426
Polymers38,7942
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area11380 Å2
ΔGint-86 kcal/mol
Surface area15800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.088, 69.043, 50.208
Angle α, β, γ (deg.)90.000, 111.810, 90.000
Int Tables number5
Space group name H-MC121
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein putative NTP pyrophosphohydrolase


Mass: 19397.064 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Exiguobacterium sibiricum 255-15 (bacteria)
Gene: Exig_1061 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: B1YMF4
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.16 Å3/Da / Density % sol: 43.07 %
Crystal growTemperature: 277 K / pH: 7.5
Details: 1.4000M Na3Citrate, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0000,0.9798
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 30, 2007
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97981
ReflectionResolution: 1.78→39.621 Å / Num. obs: 15531 / % possible obs: 98.1 % / Redundancy: 2.8 % / Biso Wilson estimate: 21.33 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 9.8
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2-2.050.9432.431503424499.9
2.05-2.110.7882.9307714135100
2.11-2.170.6383.5299914033100
2.17-2.240.5164.2290543909100
2.24-2.310.4694.6281423791100
2.31-2.390.4025.3273373685100
2.39-2.480.3386.1265463685100
2.48-2.580.3046.6254213574100
2.58-2.70.2368.3244633432100
2.7-2.830.2158.9233563303100
2.83-2.980.16610.9224003157100
2.98-3.160.13213.1211583043100
3.16-3.380.1115.2197662688100
3.38-3.650.09218.1184252516100
3.65-40.07721.7170342343100
4-4.470.06324.8154892147100
4.47-5.160.0624.6135431894100
5.16-6.320.06720.7116061650100
6.32-8.940.05623.888951300100
8.94-29.70.04824.74719765100

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0110refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.25data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.78→39.62 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.454 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.129
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 1,2-ETHANEDIOL (EDO) MOLECULES FROM THE CRYOPROTECTION SOLUTION WERE MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.222 788 5.1 %RANDOM
Rwork0.177 ---
obs0.179 15531 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.66 Å2
Baniso -1Baniso -2Baniso -3
1-2.57 Å20 Å20.82 Å2
2---0.84 Å20 Å2
3----1.12 Å2
Refinement stepCycle: LAST / Resolution: 1.78→39.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1321 0 8 141 1470
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221381
X-RAY DIFFRACTIONr_bond_other_d0.0010.02943
X-RAY DIFFRACTIONr_angle_refined_deg1.2981.9641875
X-RAY DIFFRACTIONr_angle_other_deg0.8532311
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8815172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.62425.30366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.43815227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.22156
X-RAY DIFFRACTIONr_chiral_restr0.080.2201
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211554
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02262
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_it1.7683859
X-RAY DIFFRACTIONr_mcbond_other0.4853339
X-RAY DIFFRACTIONr_mcangle_it2.90451387
X-RAY DIFFRACTIONr_scbond_it5.0378522
X-RAY DIFFRACTIONr_scangle_it7.65811488
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.78→1.83 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 47 -
Rwork0.354 1082 -
obs--97.58 %
Refinement TLS params.Method: refined / Origin x: -4.05 Å / Origin y: 17.88 Å / Origin z: 19.972 Å
111213212223313233
T0.1407 Å2-0.0075 Å20.0422 Å2-0.0096 Å20.0022 Å2--0.0341 Å2
L0.672 °2-0.0332 °2-0.4488 °2-0.8813 °20.1025 °2--1.1449 °2
S0.0105 Å °-0.0248 Å °-0.0082 Å °0.01 Å °0.0255 Å °-0.0488 Å °-0.0634 Å °0.0751 Å °-0.0361 Å °

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