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Basic information

Entry
Database: PDB / ID: 2anu
TitleCrystal structure of Predicted metal-dependent phosphoesterase (PHP family) (tm0559) from THERMOTOGA MARITIMA at 2.40 A resolution
Componentshypothetical protein TM0559
KeywordsMETAL BINDING PROTEIN / tm0559 / Predicted metal-dependent phosphoesterase (PHP family) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


5'-3' RNA exonuclease activity / 5'-3' DNA exonuclease activity / metal ion binding
Similarity search - Function
: / Polymerase/histidinol phosphatase, N-terminal / DNA polymerase alpha chain like domain / Polymerase/histidinol phosphatase-like / Metal-dependent hydrolases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Polymerase/histidinol phosphatase N-terminal domain-containing protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Predicted metal-dependent phosphoesterase (PHP family) (tm0559) from THERMOTOGA MARITIMA at 2.40 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / 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 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.conn_type_id / _struct_conn.id / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 300BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 ...BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THERE ARE TWO TYPES OF DIMERS IN THE ASYMMETRIC UNIT. SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SHOWS A MIXTURE OF HEXAMER AND DODECAMER (~ 4:1 HEXAMER:DODECAMER) IN SOLUTION. THE DODECAMER IS FORMED FROM TWO STACKED HEXAMERS (SEE BIOMOLECULE 1). BIOMOLECULE 2 IS EXAMPLE OF THE HEXAMER.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein TM0559
B: hypothetical protein TM0559
C: hypothetical protein TM0559
D: hypothetical protein TM0559
E: hypothetical protein TM0559
F: hypothetical protein TM0559
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,49945
Polymers182,3976
Non-polymers2,10239
Water3,819212
1
A: hypothetical protein TM0559
B: hypothetical protein TM0559
C: hypothetical protein TM0559
D: hypothetical protein TM0559
hetero molecules

A: hypothetical protein TM0559
B: hypothetical protein TM0559
C: hypothetical protein TM0559
D: hypothetical protein TM0559
hetero molecules

A: hypothetical protein TM0559
B: hypothetical protein TM0559
C: hypothetical protein TM0559
D: hypothetical protein TM0559
hetero molecules


Theoretical massNumber of molelcules
Total (without water)368,99790
Polymers364,79412
Non-polymers4,20378
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
2
E: hypothetical protein TM0559
F: hypothetical protein TM0559
hetero molecules

E: hypothetical protein TM0559
F: hypothetical protein TM0559
hetero molecules

E: hypothetical protein TM0559
F: hypothetical protein TM0559
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,49945
Polymers182,3976
Non-polymers2,10239
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area17590 Å2
ΔGint-1174 kcal/mol
Surface area48530 Å2
MethodPISA, PQS
3
A: hypothetical protein TM0559
B: hypothetical protein TM0559
hetero molecules

A: hypothetical protein TM0559
B: hypothetical protein TM0559
hetero molecules

A: hypothetical protein TM0559
B: hypothetical protein TM0559
hetero molecules

C: hypothetical protein TM0559
D: hypothetical protein TM0559
E: hypothetical protein TM0559
F: hypothetical protein TM0559
hetero molecules

C: hypothetical protein TM0559
D: hypothetical protein TM0559
E: hypothetical protein TM0559
F: hypothetical protein TM0559
hetero molecules

C: hypothetical protein TM0559
D: hypothetical protein TM0559
E: hypothetical protein TM0559
F: hypothetical protein TM0559
hetero molecules


Theoretical massNumber of molelcules
Total (without water)553,496135
Polymers547,19118
Non-polymers6,305117
Water32418
TypeNameSymmetry operationNumber
crystal symmetry operation7_544x+1/3,y-1/3,z-1/31
crystal symmetry operation8_654-y+4/3,x-y+2/3,z-1/31
crystal symmetry operation9_554-x+y+1/3,-x+2/3,z-1/31
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area56850 Å2
ΔGint-3465 kcal/mol
Surface area139000 Å2
MethodPISA
4
A: hypothetical protein TM0559
B: hypothetical protein TM0559
hetero molecules

A: hypothetical protein TM0559
B: hypothetical protein TM0559
hetero molecules

A: hypothetical protein TM0559
B: hypothetical protein TM0559
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,49945
Polymers182,3976
Non-polymers2,10239
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
MethodPQS
5
C: hypothetical protein TM0559
D: hypothetical protein TM0559
hetero molecules

C: hypothetical protein TM0559
D: hypothetical protein TM0559
hetero molecules

C: hypothetical protein TM0559
D: hypothetical protein TM0559
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,49945
Polymers182,3976
Non-polymers2,10239
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)111.307, 111.307, 383.222
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / Refine code: 4

Dom-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1LYSLYSAA5 - 23317 - 245
2LYSLYSBB5 - 23317 - 245
3ARGARGCC5 - 23217 - 244
4ARGARGDD5 - 23217 - 244
5ARGARGEE5 - 23217 - 244
6LYSLYSFF5 - 23317 - 245
DetailsTHERE ARE TWO TYPES OF DIMERS IN THE ASYMMETRIC UNIT. SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SHOWS A MIXTURE OF HEXAMER AND DODECAMER (~ 4:1 HEXAMER:DODECAMER) IN SOLUTION. THE DODECAMER IS FORMED FROM TWO STACKED HEXAMERS (SEE BIOMOLECULE 1). BIOMOLECULE 2 IS EXAMPLE OF THE HEXAMER.

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Components

#1: Protein
hypothetical protein TM0559 / Predicted metal-dependent phosphoesterase (PHP family)


Mass: 30399.514 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: tm0559 / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 / References: UniProt: Q9WZ29
#2: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.92 Å3/Da / Density % sol: 57.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6.5
Details: 0.1M KH2PO4, 2.0M NaCl, 0.1M NaH2PO4, 0.1M MES , pH 6.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL11-110.95369
SYNCHROTRONSSRL BL9-220.89194, 0.97944
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDApr 8, 2005flat mirror
MARMOSAIC 325 mm CCD2CCDMar 31, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE CRYSTAL SI(111) BENT MONOCHROMATOR (HORIZONTAL FOCUSING)SINGLE WAVELENGTHMx-ray1
2DOUBLE CRYSTAL MONOCHROMATORMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.953691
20.891941
30.979441
ReflectionResolution: 2.26→29.1 Å / Num. obs: 83429 / % possible obs: 99.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.13 / Rsym value: 0.13 / Net I/σ(I): 4.5
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsRsym value
2.26-2.3299.42.80.707162110.707
2.32-2.3899.52.80.5841.260210.584
2.38-2.4599.42.80.511.458300.51
2.45-2.5399.22.80.4361.656590.436
2.53-2.6199.32.80.3841.955220.384
2.61-2.799.32.80.3032.452930.303
2.7-2.899.62.80.2562.851680.256
2.8-2.9299.52.80.2163.449270.216
2.92-3.0599.32.80.175447250.175
3.05-3.299.42.80.1265.645460.126
3.2-3.3799.42.80.1026.942760.102
3.37-3.5799.12.70.085840690.085
3.57-3.8299.93.70.1274.838350.127
3.82-4.1399.95.40.144.736060.14
4.13-4.5299.85.30.0986.832710.098
4.52-5.051005.10.0927.330000.092
5.05-5.841005.40.116.126280.11
5.84-7.151005.30.1066.222240.106
7.15-10.111005.70.0610.417180.06
10.11-29.1965.50.05410.69000.054

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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
SHELXEmodel building
RefinementMethod to determine structure: MAD / Resolution: 2.4→29 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.919 / SU B: 13.655 / SU ML: 0.162 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.301 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. Missing residues - Molecule A: 1-4; 146-150; 234-243 Molecule B: 1-4; 145-152; 234-243 Molecule C: 1-4; 146-151; 233-243 Molecule D: ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. Missing residues - Molecule A: 1-4; 146-150; 234-243 Molecule B: 1-4; 145-152; 234-243 Molecule C: 1-4; 146-151; 233-243 Molecule D: 1-4; 145-152; 233-243 Molecule E: 1-4; 145-149; 233-243 Molecule F: 1-4; 145-149; 234-243
RfactorNum. reflection% reflectionSelection details
Rfree0.22 3516 5.1 %RANDOM
Rwork0.169 ---
all0.172 ---
obs-65772 99.99 %-
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: 30.366 Å2
Baniso -1Baniso -2Baniso -3
1--1.23 Å2-0.61 Å20 Å2
2---1.23 Å20 Å2
3---1.84 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10920 0 39 212 11171
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02211196
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210019
X-RAY DIFFRACTIONr_angle_refined_deg1.3491.92815181
X-RAY DIFFRACTIONr_angle_other_deg0.771323248
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.16851322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.93424.314547
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.499151956
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1291562
X-RAY DIFFRACTIONr_chiral_restr0.0760.21662
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212277
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022290
X-RAY DIFFRACTIONr_nbd_refined0.2010.22180
X-RAY DIFFRACTIONr_nbd_other0.1750.29938
X-RAY DIFFRACTIONr_nbtor_refined0.180.25337
X-RAY DIFFRACTIONr_nbtor_other0.0860.26622
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2334
X-RAY DIFFRACTIONr_metal_ion_refined0.0460.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1290.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.220.2123
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.211
X-RAY DIFFRACTIONr_mcbond_it1.86336883
X-RAY DIFFRACTIONr_mcbond_other0.55732698
X-RAY DIFFRACTIONr_mcangle_it2.18510775
X-RAY DIFFRACTIONr_scbond_it3.94785140
X-RAY DIFFRACTIONr_scangle_it5.222114406
Refine LS restraints NCS

Ens-ID: 1 / Number: 3369 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.30.5
2BMEDIUM POSITIONAL0.40.5
3CMEDIUM POSITIONAL0.30.5
4DMEDIUM POSITIONAL0.340.5
5EMEDIUM POSITIONAL0.370.5
6FMEDIUM POSITIONAL0.30.5
1AMEDIUM THERMAL0.722
2BMEDIUM THERMAL0.722
3CMEDIUM THERMAL0.662
4DMEDIUM THERMAL0.722
5EMEDIUM THERMAL0.692
6FMEDIUM THERMAL1.22
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 250 -
Rwork0.209 4928 -
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)
11.245-0.1126-0.04011.7315-0.2421.78190.0105-0.0757-0.03480.0448-0.0194-0.03220.06680.0850.0089-0.12430.0133-0.0123-0.1221-0.0145-0.165313.769433.767566.5991
21.83430.1265-0.42222.1451-0.10271.38740.033-0.0343-0.0865-0.01130.0337-0.27440.02560.1294-0.0666-0.1452-0.00310.0094-0.0955-0.0292-0.095833.380663.292960.8282
31.982-0.1531-0.14692.00720.25891.48420.0130.0225-0.0544-0.0154-0.00830.28430.0066-0.1133-0.0047-0.03880.01540.0072-0.0190.0534-0.095622.578726.155426.9675
41.0530.16860.28571.72920.20081.89730.00090.03680.0102-0.03820.00570.1418-0.1149-0.0833-0.0066-0.0440.02320.0402-0.03080.028-0.146832.232356.110821.6048
51.7629-0.1428-0.09811.79910.38441.44970.03290.010.0337-0.00750.01050.1019-0.0829-0.0979-0.0433-0.11980.02170.0426-0.15040.0303-0.104337.454960.4977-17.1194
62.63860.06910.43872.0930.26522.26090.0553-0.00770.05770.0217-0.04860.1084-0.0598-0.1586-0.0067-0.08750.0042-0.0003-0.04550.0404-0.049822.330328.3932-22.42
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA5 - 14517 - 157
21AA151 - 233163 - 245
32BB5 - 14417 - 156
42BB153 - 233165 - 245
53CC5 - 14517 - 157
63CC152 - 232164 - 244
74DD5 - 14417 - 156
84DD153 - 232165 - 244
95EE5 - 14417 - 156
105EE150 - 232162 - 244
116FF5 - 14417 - 156
126FF150 - 233162 - 245

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