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- PDB-2g8l: Crystal structure of a duf89 family protein (ph1575) from pyrococ... -

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Basic information

Entry
Database: PDB / ID: 2g8l
TitleCrystal structure of a duf89 family protein (ph1575) from pyrococcus horikoshii at 2.04 A resolution
Components287aa long hypothetical protein
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / hydrolase activity / metal ion binding
Similarity search - Function
Uncharacterised protein PF01937, DUF89, domain 2 / Uncharacterised protein PF01937, DUF89, domain 1 / Uncharacterised protein PF01937, DUF89, domain 3 / Damage-control phosphatase PH1575-like / Glutamate Dehydrogenase; Chain A, domain 3 / Damage-control phosphatase ARMT1-like, metal-binding domain / Damage-control phosphatase ARMT1-like, metal-binding domain superfamily / Damage-control phosphatase ARMT1-like domain / Helicase, Ruva Protein; domain 3 / Rossmann fold ...Uncharacterised protein PF01937, DUF89, domain 2 / Uncharacterised protein PF01937, DUF89, domain 1 / Uncharacterised protein PF01937, DUF89, domain 3 / Damage-control phosphatase PH1575-like / Glutamate Dehydrogenase; Chain A, domain 3 / Damage-control phosphatase ARMT1-like, metal-binding domain / Damage-control phosphatase ARMT1-like, metal-binding domain superfamily / Damage-control phosphatase ARMT1-like domain / Helicase, Ruva Protein; domain 3 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Unknown ligand / : / Damage-control phosphatase PH1575
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.04 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (3258004) from Pyrococcus horikoshii at 2.04 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A HEXAMER AS A BIOLOGICALLY SIGNIFICANT OLIGIMERIZATION STATE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 287aa long hypothetical protein
B: 287aa long hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3729
Polymers69,0612
Non-polymers3107
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-10 kcal/mol
Surface area23880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.859, 88.859, 81.499
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A HEXAMER AS A BIOLOGICALLY SIGNIFICANT OLIGIMERIZATION STATE.

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Components

#1: Protein 287aa long hypothetical protein


Mass: 34530.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: 3258004 / Production host: Escherichia coli (E. coli) / References: GenBank: 3258004, UniProt: O59272*PLUS
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.73 Å3/Da / Density % sol: 54.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 4
Details: 10.0% MPD, 0.1M Citrate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0000, 0.9796, 0.9797
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2005
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97961
30.97971
ReflectionResolution: 2.04→40.76 Å / Num. obs: 45685 / % possible obs: 99.7 % / Redundancy: 3.78 % / Biso Wilson estimate: 38.086 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 12.28
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.04-2.113.390.4372.9313092392596.9
2.11-2.20.3034.717825465895.4
2.2-2.30.2425.816746436696.7
2.3-2.420.1817.517033443497.5
2.42-2.570.1399.217173446898.3
2.57-2.770.10211.717523454598.5
2.77-3.040.07814.416947439799.3
3.04-3.480.05618.117785463099.6
3.480.04821.917412458999.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT1.701data extraction
XDSdata reduction
SHELXphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.04→39.01 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.957 / SU B: 6.881 / SU ML: 0.093 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.126
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. THERE IS ONE UNKNOWN LIGAND NEAR THE PUTATIVE ACTIVE SITE (CLOSE TO ASP156) FOR EACH MONOMER. 3. A MET-INHIBITION PROTOCOL WAS USED ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. THERE IS ONE UNKNOWN LIGAND NEAR THE PUTATIVE ACTIVE SITE (CLOSE TO ASP156) FOR EACH MONOMER. 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 0.7 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.182 2287 5 %RANDOM
Rwork0.144 ---
obs0.146 45659 99.69 %-
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: 32.674 Å2
Baniso -1Baniso -2Baniso -3
1-1.38 Å20.69 Å20 Å2
2--1.38 Å20 Å2
3----2.07 Å2
Refinement stepCycle: LAST / Resolution: 2.04→39.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4442 0 36 306 4784
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224616
X-RAY DIFFRACTIONr_bond_other_d0.0010.024453
X-RAY DIFFRACTIONr_angle_refined_deg1.3451.9916226
X-RAY DIFFRACTIONr_angle_other_deg0.767310355
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8945601
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.5924.974193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12415894
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0111526
X-RAY DIFFRACTIONr_chiral_restr0.080.2731
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025075
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02879
X-RAY DIFFRACTIONr_nbd_refined0.2130.2970
X-RAY DIFFRACTIONr_nbd_other0.1670.24473
X-RAY DIFFRACTIONr_nbtor_refined0.1760.22294
X-RAY DIFFRACTIONr_nbtor_other0.0830.22830
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2244
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2010.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.28
X-RAY DIFFRACTIONr_mcbond_it2.21932994
X-RAY DIFFRACTIONr_mcbond_other0.52631176
X-RAY DIFFRACTIONr_mcangle_it3.04554680
X-RAY DIFFRACTIONr_scbond_it5.62981809
X-RAY DIFFRACTIONr_scangle_it8.029111529
LS refinement shellResolution: 2.04→2.093 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 172 -
Rwork0.212 3056 -
obs-3228 96.01 %
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)
10.7186-0.66680.70540.9778-0.56111.18210.10220.0041-0.02580.0098-0.0557-0.0036-0.0166-0.12-0.0465-0.00960.0271-0.0073-0.04030.0132-0.030639.50868.96731.365
22.3908-0.0216-1.20211.1114-0.1483.8965-0.0390.1916-0.20590.1330.02170.18770.3051-0.60890.0174-0.05750.00530.0237-0.0272-0.0108-0.038315.08869.20637.088
31.0392-1.42120.77852.2646-0.5691.34890.12250.0626-0.0035-0.087-0.1565-0.06620.21810.07950.0340.05550.0088-0.0235-0.09380.0034-0.042949.47957.335.423
40.70670.5461-0.15722.08850.44823.2475-0.02750.00390.0396-0.0837-0.0608-0.06110.00120.05090.0883-0.09560.0653-0.0179-0.11550.0072-0.038554.53239.49318.249
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA0 - 6712 - 79
22AA68 - 28480 - 296
33BB2 - 6714 - 79
44BB68 - 28780 - 299

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