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- PDB-9y1l: Crystal Structure of Putative Restriction Endonuclease Domain-Con... -

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Basic information

Entry
Database: PDB / ID: 9y1l
TitleCrystal Structure of Putative Restriction Endonuclease Domain-Containing Protein from Leptospirillum ferriphilum YSK
ComponentsPutative restriction endonuclease domain-containing protein
KeywordsHYDROLASE / Restriction endonuclease / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homologyPutative restriction endonuclease / Nuclease, putative, TT1808 / Putative restriction endonuclease / Restriction endonuclease type II-like / FORMIC ACID / Putative restriction endonuclease domain-containing protein
Function and homology information
Biological speciesLeptospirillum ferriphilum YSK (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsKim, Y. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Crystal Structure of Putative Restriction Endonuclease Domain-Containing Protein from Leptospirillum ferriphilum YSK
Authors: Kim, Y. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionAug 29, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative restriction endonuclease domain-containing protein
B: Putative restriction endonuclease domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3276
Polymers42,1762
Non-polymers1524
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-27 kcal/mol
Surface area14430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.989, 76.989, 45.840
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Putative restriction endonuclease domain-containing protein


Mass: 21087.783 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Y981_08535, Putative Restriction Endonuclease Domain-Containing Protein
Source: (gene. exp.) Leptospirillum ferriphilum YSK (bacteria)
Gene: BOX24_03850, LptCag_1749 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A094W816
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 1.86 Å3/Da / Density % sol: 33.86 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: Unknown

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97931 Å
DetectorType: SBC-3 / Detector: CCD / Date: Jul 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.5539
pseudo-merohedral22K, H, -L20.4461
ReflectionResolution: 1.65→50 Å / Num. obs: 36195 / % possible obs: 98.8 % / Redundancy: 6.2 % / Biso Wilson estimate: 22.5 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.026 / Rrim(I) all: 0.067 / Net I/σ(I): 31.7
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 5.7 / Num. unique obs: 1568 / CC1/2: 0.912 / Rpim(I) all: 0.15 / Rrim(I) all: 0.322 / % possible all: 85.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→26.961 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 4.161 / SU ML: 0.076 / Cross valid method: FREE R-VALUE / ESU R: 0.027 / ESU R Free: 0.018
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1775 1725 4.778 %
Rwork0.1544 34377 -
all0.156 --
obs-36102 98.575 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 30.315 Å2
Baniso -1Baniso -2Baniso -3
1--5.363 Å2-0 Å2-0 Å2
2---5.363 Å2-0 Å2
3---10.726 Å2
Refinement stepCycle: LAST / Resolution: 1.65→26.961 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 8 185 2585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122532
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162390
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.8293451
X-RAY DIFFRACTIONr_angle_other_deg0.7251.7545527
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1595317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2.061524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.46110412
X-RAY DIFFRACTIONr_dihedral_angle_6_deg18.79710119
X-RAY DIFFRACTIONr_chiral_restr0.0690.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023056
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02584
X-RAY DIFFRACTIONr_nbd_refined0.1990.2456
X-RAY DIFFRACTIONr_symmetry_nbd_other0.220.22164
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21240
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21355
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0820.256
X-RAY DIFFRACTIONr_metal_ion_refined0.1190.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0870.216
X-RAY DIFFRACTIONr_nbd_other0.2580.261
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1170.26
X-RAY DIFFRACTIONr_mcbond_it6.5832.8281256
X-RAY DIFFRACTIONr_mcbond_other6.5782.8281256
X-RAY DIFFRACTIONr_mcangle_it8.4275.0721577
X-RAY DIFFRACTIONr_mcangle_other8.4245.0721578
X-RAY DIFFRACTIONr_scbond_it7.443.0471276
X-RAY DIFFRACTIONr_scbond_other7.4373.0471277
X-RAY DIFFRACTIONr_scangle_it9.4725.4551874
X-RAY DIFFRACTIONr_scangle_other9.4695.4551875
X-RAY DIFFRACTIONr_lrange_it10.9214433.1862643
X-RAY DIFFRACTIONr_lrange_other10.9314451.742632
X-RAY DIFFRACTIONr_rigid_bond_restr8.10134916
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.6920.229690.2062307X-RAY DIFFRACTION86.4
1.692-1.7390.2431310.1872394X-RAY DIFFRACTION97.265
1.739-1.7890.2331460.1862446X-RAY DIFFRACTION99.9229
1.789-1.8440.225960.1632372X-RAY DIFFRACTION99.919
1.844-1.9040.2031260.1822313X-RAY DIFFRACTION99.9181
1.904-1.9710.2161100.1862220X-RAY DIFFRACTION99.9142
1.971-2.0460.1831250.1762131X-RAY DIFFRACTION100
2.046-2.1290.166940.1732072X-RAY DIFFRACTION99.9539
2.129-2.2240.2161220.1641942X-RAY DIFFRACTION100
2.224-2.3320.1841120.161878X-RAY DIFFRACTION100
2.332-2.4580.167820.1571817X-RAY DIFFRACTION99.9474
2.458-2.6070.185860.161694X-RAY DIFFRACTION100
2.607-2.7860.19760.1651625X-RAY DIFFRACTION100
2.786-3.0090.16780.1611458X-RAY DIFFRACTION100
3.009-3.2960.178700.1521380X-RAY DIFFRACTION100
3.296-3.6840.132700.1351235X-RAY DIFFRACTION100
3.684-4.2510.159440.1121121X-RAY DIFFRACTION100
4.251-5.2020.117530.113912X-RAY DIFFRACTION99.4845
5.202-7.3340.346160.177727X-RAY DIFFRACTION100
7.334-260.203190.17333X-RAY DIFFRACTION85.0242
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)
10.00820.01630.01080.2202-0.13140.22580.004-0.0150.007-0.0347-0.039-0.0190.00260.01670.0350.0222-0.0130.00450.0373-0.0090.0396-35.834.3594-0.0762
20.34290.13910.05120.2037-0.13110.16460.0186-0.044-0.0433-0.0034-0.0052-0.01250.0105-0.0178-0.01350.0342-0.0043-0.00090.021-0.01540.0374-16.9932-5.6571-13.8737
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA38 - 188
2X-RAY DIFFRACTION1ALLB36 - 188

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