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- PDB-3mzo: Crystal structure of a HD-domain phosphohydrolase (lin2634) from ... -

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Basic information

Entry
Database: PDB / ID: 3mzo
TitleCrystal structure of a HD-domain phosphohydrolase (lin2634) from LISTERIA INNOCUA at 1.98 A resolution
ComponentsLin2634 protein
KeywordsHYDROLASE / HD-domain phosphohydrolase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology5'-deoxynucleotidase YfbR-like / Hypothetical protein af1432 / Hypothetical protein af1432 / Orthogonal Bundle / Mainly Alpha / metal ion binding / DI(HYDROXYETHYL)ETHER / Lin2634 protein
Function and homology information
Biological speciesListeria innocua (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.98 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a HD-domain phosphohydrolase (lin2634) from LISTERIA INNOCUA at 1.98 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 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: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lin2634 protein
B: Lin2634 protein
C: Lin2634 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,15916
Polymers75,5063
Non-polymers65313
Water6,756375
1
A: Lin2634 protein
B: Lin2634 protein
C: Lin2634 protein
hetero molecules

A: Lin2634 protein
B: Lin2634 protein
C: Lin2634 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,31832
Polymers151,0126
Non-polymers1,30626
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area24280 Å2
ΔGint-307 kcal/mol
Surface area46870 Å2
MethodPISA
2
A: Lin2634 protein
hetero molecules

A: Lin2634 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,03016
Polymers50,3372
Non-polymers69314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5290 Å2
ΔGint-115 kcal/mol
Surface area18870 Å2
MethodPISA
3
B: Lin2634 protein
C: Lin2634 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6448
Polymers50,3372
Non-polymers3076
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-74 kcal/mol
Surface area18110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.243, 121.866, 66.621
Angle α, β, γ (deg.)90.000, 121.360, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-684-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 4 / Auth seq-ID: 1 - 208 / Label seq-ID: 2 - 209

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

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Components

#1: Protein Lin2634 protein


Mass: 25168.629 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua (bacteria) / Gene: lin2634 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q928A2
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.32 Å3/Da / Density % sol: 47.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2000M calcium chloride, 28.0000% polyethylene glycol 400, 0.1M HEPES pH 7.5, 0.005M 2'-deoxyadenosine 5'-monophosphate (dAMP), NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97939,0.97925
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 11, 2010 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979391
30.979251
ReflectionResolution: 1.98→48.741 Å / Num. obs: 47810 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 29.174 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 15.73
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.98-2.050.5042.717620468499.5
2.05-2.130.3563.817691469499.6
2.13-2.230.2655.118544490999.7
2.23-2.350.2086.418394485899.6
2.35-2.490.1369.317274456699.5
2.49-2.690.112.218763494199.6
2.69-2.960.06717.218070477099.4
2.96-3.380.04423.617733469799.3
3.38-4.250.02735.218109479199.2
4.25-48.7410.02741.218090487598.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.98→48.741 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 6.819 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.14
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 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. POLYETHYLENE GLYCOL (PEG), CALCIUM (CA) MODELED ARE PRESENT IN CRYSTALLIZATION/CRYO CANDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2 2418 5.1 %RANDOM
Rwork0.166 ---
obs0.167 47810 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.44 Å2 / Biso mean: 36.888 Å2 / Biso min: 5.38 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20 Å2-0.41 Å2
2---0.86 Å20 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 1.98→48.741 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4965 0 25 375 5365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225220
X-RAY DIFFRACTIONr_bond_other_d0.0020.023551
X-RAY DIFFRACTIONr_angle_refined_deg1.4011.9697074
X-RAY DIFFRACTIONr_angle_other_deg0.95638730
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4215655
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.35625.349258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60915956
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0541517
X-RAY DIFFRACTIONr_chiral_restr0.090.2774
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025797
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021029
X-RAY DIFFRACTIONr_mcbond_it1.6233133
X-RAY DIFFRACTIONr_mcbond_other0.71631263
X-RAY DIFFRACTIONr_mcangle_it2.7955081
X-RAY DIFFRACTIONr_scbond_it4.49182087
X-RAY DIFFRACTIONr_scangle_it6.413111972
Refine LS restraints NCS

Ens-ID: 1 / Number: 2445 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.360.5
2BMEDIUM POSITIONAL0.50.5
3CMEDIUM POSITIONAL0.420.5
1AMEDIUM THERMAL1.242
2BMEDIUM THERMAL1.282
3CMEDIUM THERMAL1.122
LS refinement shellResolution: 1.98→2.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 174 -
Rwork0.229 3354 -
all-3528 -
obs--99.52 %
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)
11.1415-0.0011-0.7060.4608-0.27091.45670.0452-0.21910.08120.07710.0135-0.0766-0.04840.2194-0.05870.0326-0.0065-0.01690.0526-0.02260.02375.462583.840810.5654
20.955-0.2706-0.15471.2769-0.09960.63020.03440.00160.1621-0.1046-0.0041-0.1964-0.12360.1407-0.03030.0698-0.01430.01750.05150.01710.107925.046560.19751.0717
31.7383-0.2492-0.51890.8030.12260.77520.003-0.0696-0.13560.02-0.00230.05330.12360.0001-0.00070.07210.0077-0.02260.03610.03580.057512.283344.90412.4995
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 209
2X-RAY DIFFRACTION2B1 - 211
3X-RAY DIFFRACTION3C0 - 210

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