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- PDB-3son: Crystal structure of a putativel NUDIX hydrolase (LMOf2365_2679) ... -

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Database: PDB / ID: 3son
TitleCrystal structure of a putativel NUDIX hydrolase (LMOf2365_2679) from Listeria monocytogenes str. 4b F2365 at 1.70 A resolution
ComponentsHypothetical NUDIX hydrolase
KeywordsHYDROLASE / Nudix / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyNucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Alpha-Beta Complex / Alpha Beta / :
Function and homology information
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.71 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Hypothetical NUDIX hydrolase (LMOf2365_2679) from LISTERIA MONOCYTOGENES (ATCC 19115) at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 1, 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_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.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.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_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

Downloads & links

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Assembly

Deposited unit
A: Hypothetical NUDIX hydrolase
B: Hypothetical NUDIX hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8784
Polymers34,7982
Non-polymers802
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-30 kcal/mol
Surface area14490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.880, 57.880, 94.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A0 - 26
2115B0 - 26
1216A26 - 33
2216B26 - 33
1315A34 - 54
2315B34 - 54
1416A51 - 55
2416B51 - 55
1515A56 - 97
2515B56 - 97
1615A115 - 123
2615B115 - 123
1715A132 - 143
2715B132 - 143
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION

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Components

#1: Protein Hypothetical NUDIX hydrolase / MutT/nudix family protein


Mass: 17398.807 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: Li 2 / Gene: LMOf2365_2679 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q71W72
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Sequence details1. THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...1. 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. 2. THE STRAIN CLONED (ATCC 19115 / 4b / Li 2) DIFFERS FROM THE STRAIN SEQUENCED IN THE DATABASE REFERENCE (serotype 4b strain F2365). DNA SEQUENCING OF THE CLONED CONSTRUCT SHOWS AN ISOLUCINE AT POSITION 121 INSTEAD OF A VALINE. THE ISOLUCINE AT POSITION 121 IS SUPPORTED BY THE ELECTRON DENSITY.

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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: 2.27 Å3/Da / Density % sol: 45.92 %
Description: The crystal was larger than the beam. After collecting the 3-wavelength MAD data set, the crystal was translated to place a fresh part of the crystal in the beam before collecting the ...Description: The crystal was larger than the beam. After collecting the 3-wavelength MAD data set, the crystal was translated to place a fresh part of the crystal in the beam before collecting the data used in refinement.
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 10.0% 2-propanol, 0.2M Ca(OAc)2, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97937,0.97908
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 19, 2007
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979371
30.979081
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.738
11-H, K, -L20.262
ReflectionResolution: 1.7→27.671 Å / Num. obs: 34048 / % possible obs: 99 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 26.769 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 13.88
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.7-1.753.70.4263.19160247699.8
1.75-1.793.70.3653.79182245099.6
1.79-1.853.70.2844.88975239599.8
1.85-1.93.70.2975.18649230999.4
1.9-1.963.70.1568.28269222599.8
1.96-2.033.80.1259.98122216299.8
2.03-2.114.60.11412.99624209099.6
2.11-2.25.30.10216.110783203499.7
2.2-2.295.70.11616.511037193599.9
2.29-2.416.50.0822.611938184199.9
2.41-2.547.50.07426.913286178299.9
2.54-2.697.40.06231.3122371649100
2.69-2.887.40.05235.311698157799.8
2.88-3.117.40.04840.110738145399.9
3.11-3.47.40.04343.9100911364100
3.4-3.87.40.04345.58987122099.8
3.8-4.397.20.03647.47612106099.7
4.39-5.386.90.03347.3642292599.9
5.38-7.6170.03747.3506972099.9
7.61-27.675.60.03342.2211638095.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEJune 12, 2007data scaling
REFMAC5.6.0116refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.71→27.671 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / Occupancy max: 1 / Occupancy min: 0.19 / SU B: 4.509 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. A MET-INHIBITION ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. SOLVENT MOLECULES WERE EXCLUDED FROM THE AUTOMATIC ASSIGNMENT OF THE TLS GROUPS. 5. THE DIFFRACTION DATA SHOW MEROHEDERAL TWINNING WITH TWIN LAW "-H, K, -L". THE REFINED TWIN FRACTION WAS 0.26. THE R-FREE TEST SET REFLECTIONS WERE CHOSEN AT RANDOM WITH THE TWIN LAW INCLUDED. 6. BOTH SODIUM AND CALCIUM ARE PRESENT IN THE CRYSTALLIZATION SOLUTION / PROTEIN BUFFER. CALCIUM WAS MODELED BASED ON A SLIGHTLY BETTER FIT TO THE DENSITY BUT THE SITE COULD BE MIXED NA AND CA. 7. THE RAMACHANDRAN OUTLIER A60 IS IN A LOOP WITH WEAK ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.196 1742 5.2 %RANDOM + TWIN LAW
Rwork0.1634 ---
obs0.1651 33655 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.07 Å2 / Biso mean: 31.6546 Å2 / Biso min: 16.72 Å2
Baniso -1Baniso -2Baniso -3
1-14.38 Å20 Å20 Å2
2--14.38 Å20 Å2
3----28.75 Å2
Refinement stepCycle: LAST / Resolution: 1.71→27.671 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2341 0 2 169 2512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022446
X-RAY DIFFRACTIONr_bond_other_d0.0010.021580
X-RAY DIFFRACTIONr_angle_refined_deg1.5651.9523333
X-RAY DIFFRACTIONr_angle_other_deg0.90133863
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1965300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.29725120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.75315373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.448158
X-RAY DIFFRACTIONr_chiral_restr0.1030.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022766
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02510
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
612MEDIUM POSITIONAL0.220.5
930LOOSE POSITIONAL0.495
612MEDIUM THERMAL4.792
930LOOSE THERMAL3.9210
LS refinement shellResolution: 1.706→1.75 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 106 -
Rwork0.161 2320 -
all-2426 -
obs--97.82 %
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)
10.9808-0.0012-0.4230.9541-0.33371.1460.0030.13090.0282-0.00320.07280.1048-0.0607-0.1024-0.07580.00470.0038-0.00190.05490.03720.152620.9757.79261.748
20.65920.1856-0.00451.2063-0.16341.39990.0941-0.02210.04460.0665-0.04170.1051-0.15010.1413-0.05240.0364-0.01550.04390.01680.00640.151817.9728.09289.607
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 148
2X-RAY DIFFRACTION2B3 - 148

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