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- PDB-2ffj: CRYSTAL STRUCTURE OF a DUF89 family protein (AF1104) FROM ARCHAEO... -

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Basic information

Entry
Database: PDB / ID: 2ffj
TitleCRYSTAL STRUCTURE OF a DUF89 family protein (AF1104) FROM ARCHAEOGLOBUS FULGIDUS DSM 4304 AT 2.45 A RESOLUTION
Componentsconserved 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
: / Damage-control phosphatase AF_1104
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.45 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of (2649480) from ARCHAEOGLOBUS FULGIDUS at 2.45 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_obs
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: conserved hypothetical protein
B: conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,33811
Polymers67,5342
Non-polymers8049
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: conserved hypothetical protein
hetero molecules

A: conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,33811
Polymers67,5342
Non-polymers8049
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_564-x+1/2,-y+1,z-1/21
Buried area2730 Å2
ΔGint-138 kcal/mol
Surface area23280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.806, 80.677, 120.868
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11CYSILEAA10 - 10822 - 120
21CYSILEBB10 - 10822 - 120
32VALLEUAA123 - 252135 - 264
42VALLEUBB123 - 252135 - 264
53LEUVALAA257 - 287269 - 299
63SERVALBB256 - 287268 - 299

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Components

#1: Protein conserved hypothetical protein


Mass: 33766.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: 2649480 / Production host: Escherichia coli (E. coli) / References: GenBank: 2649480, UniProt: O29161*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 4.2
Details: 2.0M ammonium sulfate, 0.1M Phosphate Citrate, pH 4.2, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97932, 0.97918, 0.91837
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 4, 2005
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979321
20.979181
30.918371
ReflectionResolution: 2.45→29.9 Å / Num. obs: 25288 / % possible obs: 99.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 6.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsRsym value
2.45-2.511003.70.6571.118580.657
2.51-2.581003.70.5691.317930.569
2.58-2.661003.70.4851.517730.485
2.66-2.741003.70.3851.816860.385
2.74-2.831003.70.3222.316440.322
2.83-2.931003.70.249316030.249
2.93-3.041003.70.1814.115590.181
3.04-3.161003.70.1524.814880.152
3.16-3.31003.70.1255.714450.125
3.3-3.4699.93.70.0947.413610.094
3.46-3.6599.93.70.088.613270.08
3.65-3.8799.83.70.078.512270.07
3.87-4.1499.73.70.0649.111560.064
4.14-4.4799.63.60.05710.711040.057
4.47-4.999.53.60.05211.29990.052
4.9-5.4899.33.70.0539.99140.053
5.48-6.3399.13.60.06210.38190.062
6.33-7.7598.63.50.05511.56880.055
7.75-10.9698.13.50.03915.95440.039
10.96-29.990.93.20.0511.33000.05

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT1.601data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.45→29.9 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.917 / SU B: 17.201 / SU ML: 0.189 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.36 / ESU R Free: 0.267
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 0.7 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. BOTH PHOSPHATE AND SULFATE IONS ARE PRESENT IN THE CRYSTALLIZATION SOLUTION; SO4 WERE MODELLED INTO DENSITY DUE TO ITS HIGHER CONCENTRATION. IT IS NOT POSSIBLE TO ASSIGNED THE TRUE IDENTITIES OF THESE IONS BASED ON DENSITIY MAP. 4. A43-49, A115-122, A253-257, B43-49, B113-B120 AS WELL AS N-TERMINI ARE NOT PRESENT IN THE MODEL. THERE ARE SOME DISORDERED DENSITIES FOR THE LOOPS BETWEEN A114-123, B110-127 AND A253-257. 5. TWO ATOMS ASSIGNED AS WATERS 98 AND 99 ARE LOCATED IN THE ACTIVE SITES, THE CORRESPONDING ATOMS IN THE STRUCTURAL HOMOLOG 1XFI ARE MAGNESIUM IONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1288 5.1 %RANDOM
Rwork0.189 ---
all0.192 ---
obs0.19189 23975 99.43 %-
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: 47.777 Å2
Baniso -1Baniso -2Baniso -3
1-1.83 Å20 Å20 Å2
2---1.78 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.45→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4066 0 41 89 4196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224136
X-RAY DIFFRACTIONr_bond_other_d0.0020.023956
X-RAY DIFFRACTIONr_angle_refined_deg1.392.0015591
X-RAY DIFFRACTIONr_angle_other_deg0.80139134
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0395531
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.5124.451164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.53115747
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2731531
X-RAY DIFFRACTIONr_chiral_restr0.0690.2676
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024527
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02764
X-RAY DIFFRACTIONr_nbd_refined0.2260.2942
X-RAY DIFFRACTIONr_nbd_other0.1680.23914
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22059
X-RAY DIFFRACTIONr_nbtor_other0.0870.22705
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2132
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3070.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1950.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0580.22
X-RAY DIFFRACTIONr_mcbond_it1.60532742
X-RAY DIFFRACTIONr_mcbond_other0.32931091
X-RAY DIFFRACTIONr_mcangle_it2.37254288
X-RAY DIFFRACTIONr_scbond_it4.77681525
X-RAY DIFFRACTIONr_scangle_it7111303
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
1510tight positional0.070.05
2294medium positional0.410.5
1510tight thermal0.130.5
2294medium thermal0.712
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 98 -
Rwork0.269 1756 -
obs--99.95 %
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)
16.81042.92072.12359.61171.16883.328-0.0651-0.0129-0.4596-0.05610.302-0.09680.1430.1394-0.2369-0.1226-0.0604-0.009-0.1280.0139-0.18074.94612.77682.644
22.6087-0.73660.93322.7812-0.19683.5537-0.0109-0.0937-0.15460.29060.0293-0.28690.16890.2182-0.0183-0.14330.0047-0.0508-0.12610.0053-0.052120.42416.123103.659
32.3504-2.5776-0.69326.60032.20625.9277-0.0470.00290.2825-0.04790.2617-0.1038-0.35440.0015-0.2148-0.15770.0265-0.0278-0.14230.0164-0.14488.78142.70795.203
41.80430.5186-1.17423.3-1.34483.9605-0.0150.17140.0222-0.36390.1550.03750.0032-0.1102-0.14-0.1428-0.04840.0233-0.1133-0.0226-0.132113.38939.11569.85
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 6819 - 80
2X-RAY DIFFRACTION2AA69 - 28881 - 300
3X-RAY DIFFRACTION3BB7 - 6819 - 80
4X-RAY DIFFRACTION4BB69 - 28881 - 300

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