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- PDB-1zup: CRYSTAL STRUCTURE OF A PUTATIVE NUCLEASE WITH A RIBONUCLEASE H-LI... -

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Basic information

Entry
Database: PDB / ID: 1zup
TitleCRYSTAL STRUCTURE OF A PUTATIVE NUCLEASE WITH A RIBONUCLEASE H-LIKE MOTIF FOLD (TM1739) FROM THERMOTOGA MARITIMA AT 2.20 A RESOLUTION
Componentshypothetical protein TM1739
KeywordsHYDROLASE / PUTATIVE NUCLEASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI
Function / homologyNurA domain / NurA domain / NurA / Ribonuclease H-like superfamily / NurA domain-containing protein
Function and homology information
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (tm1739) from Thermotoga maritima at 2.20 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 31, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein TM1739
B: hypothetical protein TM1739


Theoretical massNumber of molelcules
Total (without water)73,4402
Polymers73,4402
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-14 kcal/mol
Surface area26150 Å2
MethodPISA
2
A: hypothetical protein TM1739
B: hypothetical protein TM1739

A: hypothetical protein TM1739
B: hypothetical protein TM1739


Theoretical massNumber of molelcules
Total (without water)146,8804
Polymers146,8804
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area12090 Å2
ΔGint-44 kcal/mol
Surface area50260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.433, 82.433, 234.492
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-310-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 5

Dom-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1HISILEAA-1 - 30111 - 313
2ARGGLYBB4 - 30216 - 314

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Components

#1: Protein hypothetical protein TM1739


Mass: 36719.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: tm1739 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X261
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.1861.04
2
Crystal grow
Temperature (K)Crystal-IDMethodDetails
2771vapor diffusion, sitting drop, nanodrop0.10M Acetate_Na, 0.03M HCl, 8.00% MPD, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
2772vapor diffusion, sitting drop, nanodrop0.10M Acetate_Na, 0.03M HCl, 7.00% MPD, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.211
SYNCHROTRONALS 8.2.120.9794
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDDec 20, 2003Double crystal Si(111)
ADSC QUANTUM 2102CCDJan 8, 2004Double crystal Si(111)
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97941
ReflectionResolution: 2.1→41.22 Å / Num. obs: 48259 / % possible obs: 100 % / Redundancy: 9.2 % / Rsym value: 0.121 / Net I/σ(I): 5.5
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.01375 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3519 / Rsym value: 0.01375 / % possible all: 100

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
SCALAdata scaling
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.925 / SU B: 13.656 / SU ML: 0.168 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.23 / ESU R Free: 0.2
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE ELECTRON DENSITY OF APPROXIMATELY HALF OF MOLECULE B IS POOR, AND THE MODEL WAS BUILT BASED ON MOLECULE A. THESE POOR REGIONS INCLUDE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE ELECTRON DENSITY OF APPROXIMATELY HALF OF MOLECULE B IS POOR, AND THE MODEL WAS BUILT BASED ON MOLECULE A. THESE POOR REGIONS INCLUDE RESIDUES 160-260, 26-44 (THEY ARE IN THE SAME DOMAIN OF MOLECULE B) AND RESIDUES 78-83.
RfactorNum. reflection% reflectionSelection details
Rfree0.266 2114 5 %RANDOM
Rwork0.228 ---
all0.23 ---
obs0.22988 39863 99.93 %-
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: 60.792 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å20 Å2
2--0.42 Å20 Å2
3----0.84 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4349 0 0 70 4419
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224477
X-RAY DIFFRACTIONr_bond_other_d0.0020.024148
X-RAY DIFFRACTIONr_angle_refined_deg1.6511.9796035
X-RAY DIFFRACTIONr_angle_other_deg0.82639562
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0845584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.67224.108185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.52215766
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9781527
X-RAY DIFFRACTIONr_chiral_restr0.090.2672
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025056
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02909
X-RAY DIFFRACTIONr_nbd_refined0.2130.2877
X-RAY DIFFRACTIONr_nbd_other0.1790.24180
X-RAY DIFFRACTIONr_nbtor_refined0.1870.22158
X-RAY DIFFRACTIONr_nbtor_other0.0880.22862
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2137
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.040.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3450.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3030.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.23
X-RAY DIFFRACTIONr_mcbond_it2.42232928
X-RAY DIFFRACTIONr_mcbond_other0.65331200
X-RAY DIFFRACTIONr_mcangle_it3.51154574
X-RAY DIFFRACTIONr_scbond_it6.25581709
X-RAY DIFFRACTIONr_scangle_it8.85111461
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
1629medium positional0.260.5
2181loose positional0.645
1629medium thermal1.082
2181loose thermal2.5810
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 147 -
Rwork0.248 2857 -
obs--100 %
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)
11.32950.26660.45731.35750.81193.8628-0.07880.1542-0.0997-0.00280.0281-0.13950.47250.15030.0508-0.11640.0255-0.0054-0.3012-0.0398-0.370629.38213.805-16.154
21.5321-0.4364-0.64041.04240.7245.36830.15-0.31550.1944-0.1540.3665-0.5851-0.3722.0326-0.5165-0.2088-0.18950.07560.6066-0.1540.089257.09836.1-11.319
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 30113 - 313
2X-RAY DIFFRACTION2BB4 - 30216 - 314

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