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- PDB-3e38: CRYSTAL STRUCTURE OF A TWO-DOMAIN PROTEIN CONTAINING PREDICTED PH... -

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Basic information

Entry
Database: PDB / ID: 3.0E+38
TitleCRYSTAL STRUCTURE OF A TWO-DOMAIN PROTEIN CONTAINING PREDICTED PHP-LIKE METAL-DEPENDENT PHOSPHOESTERASE (BVU_3505) FROM BACTEROIDES VULGATUS ATCC 8482 AT 2.20 A RESOLUTION
Componentstwo-domain protein containing predicted PHP-like metal-dependent phosphoesterase
KeywordsHYDROLASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


catalytic activity / metal ion binding
Similarity search - Function
Immunoglobulin-like - #3090 / Ig-like domain / Ig-like domain / Polymerase/histidinol phosphatase, N-terminal / DNA polymerase alpha chain like domain / Polymerase/histidinol phosphatase-like / Metal-dependent hydrolases / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like ...Immunoglobulin-like - #3090 / Ig-like domain / Ig-like domain / Polymerase/histidinol phosphatase, N-terminal / DNA polymerase alpha chain like domain / Polymerase/histidinol phosphatase-like / Metal-dependent hydrolases / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
CACODYLATE ION / POLIIIAc domain-containing protein
Similarity search - Component
Biological speciesBacteroides vulgatus ATCC 8482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of two-domain protein containing predicted PHP-like metal-dependent phosphoesterase (YP_001300751.1) from Bacteroides vulgatus ATCC 8482 at 2.20 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 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_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.pdbx_dist_value / _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_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: two-domain protein containing predicted PHP-like metal-dependent phosphoesterase
B: two-domain protein containing predicted PHP-like metal-dependent phosphoesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,97313
Polymers80,0302
Non-polymers94311
Water7,764431
1
A: two-domain protein containing predicted PHP-like metal-dependent phosphoesterase
B: two-domain protein containing predicted PHP-like metal-dependent phosphoesterase
hetero molecules

A: two-domain protein containing predicted PHP-like metal-dependent phosphoesterase
B: two-domain protein containing predicted PHP-like metal-dependent phosphoesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,94526
Polymers160,0604
Non-polymers1,88522
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area11230 Å2
ΔGint-466 kcal/mol
Surface area51200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.680, 117.820, 79.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg label comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAASN1AA22 - 262 - 6
21GLYASN1BB0 - 261 - 6
32GLUASP3AA27 - 857 - 65
42GLUASP3BB27 - 857 - 65
53HISLEU5AA90 - 36370 - 343
63HISLEU5BB90 - 36370 - 343

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Components

#1: Protein two-domain protein containing predicted PHP-like metal-dependent phosphoesterase


Mass: 40014.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides vulgatus ATCC 8482 (bacteria)
Gene: YP_001300751.1, BVU_3505 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6L615
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. THE CLONED CONSTRUCT CONTAINS RESIDUES 22-363 OF THE FULL LENGTH PROTEIN.

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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: 2.8 Å3/Da / Density % sol: 56.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20.0000% Glycerol, 0.1600M Mg(oAc)2, 16.0000% PEG-8000, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 11, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→29.604 Å / Num. obs: 45776 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 31.645 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 11.94
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.2-2.280.772287898350193.2
2.28-2.370.6222.4316638579199.2
2.37-2.480.4963336338962199.3
2.48-2.610.3933.8327928689199.4
2.61-2.770.314.8325188561199
2.77-2.980.2146.8331338654199.4
2.98-3.280.12910.8339518845199.5
3.28-3.760.07418.2335578850199
3.76-4.720.03929.8331418686199.2
4.72-29.6040.03137340248827198.5

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.004data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→29.604 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.935 / SU B: 10.417 / SU ML: 0.142 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.216 / ESU R Free: 0.188
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 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 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.GLYCEROL MOLECULES FROM THE CRYSTALLIZATION CONDITIONS ARE MODELED INTO THE STRUCTURE. 5. THREE ZN IONS, WHICH CO-PURIFIED WITH THE PROTEIN, ARE MODELED IN EACH SUBUNIT OF THIS STRUCTURE. ANOMALOUS DIFFERENCE FOURIERS AND X-RAY FLUORESCENCE EXPERIMENTS SUPPORT THE ASSIGNMENT OF THE ZINC ATOMS. 6.IN THE CONSERVED ACTIVE SITES, CACODYLATE ANIONS FROM THE CRYSTALLIZATION BUFFER HAVE BEEN MODELED. THE PRESENCE OF CACODYLATE AT THESE SITES IS SUPPORTED BY ANOMALOUS DIFFERENCE FOURIERS. HOWEVER, THE SITES ARE DISORDERED AND MAY ONLY BE PARTIALLY OCCUPIED. SINCE THIS DISORDER COULD NOT BE RESOLVED, ONLY A SINGLE ORIENTATION OF CACODYLATE IS MODELED IN THE STRUCTURE, EVEN THOUGH THIS DOES NOT FULLY SATISFY THE COORDINATION GEOMETRY OF THE ZN SITES.
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2319 5.1 %RANDOM
Rwork0.172 ---
obs0.175 45753 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.905 Å2
Baniso -1Baniso -2Baniso -3
1--2.37 Å20 Å20 Å2
2---1.56 Å20 Å2
3---3.93 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.604 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5501 0 34 431 5966
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0215715
X-RAY DIFFRACTIONr_bond_other_d0.0010.023872
X-RAY DIFFRACTIONr_angle_refined_deg1.7861.9427751
X-RAY DIFFRACTIONr_angle_other_deg1.40539389
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5185695
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.72423.64283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.3315961
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2521540
X-RAY DIFFRACTIONr_chiral_restr0.080.2839
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216400
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021216
X-RAY DIFFRACTIONr_mcbond_it1.94333444
X-RAY DIFFRACTIONr_mcbond_other0.57931397
X-RAY DIFFRACTIONr_mcangle_it3.00655573
X-RAY DIFFRACTIONr_scbond_it5.7282271
X-RAY DIFFRACTIONr_scangle_it7.386112178
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A415TIGHT POSITIONAL0.080.05
B1592MEDIUM POSITIONAL0.130.5
A2492LOOSE POSITIONAL0.285
B415TIGHT THERMAL1.660.5
A1592MEDIUM THERMAL1.672
B2492LOOSE THERMAL2.2510
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 160 -
Rwork0.22 3035 -
all-3195 -
obs--94.5 %
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)
10.7732-0.14910.12570.8121-0.17890.355-0.05630.0088-0.0687-0.05450.06820.05830.0254-0.0265-0.0119-0.0841-0.02210.0048-0.0815-0.0095-0.04844.050641.16430.4923
21.0259-0.4558-0.03381.11110.34990.3635-0.1343-0.24590.05410.10720.1259-0.0681-0.05720.06130.00840.00610.0689-0.02130.052-0.005-0.097865.159853.363466.3966
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA22 - 3632 - 343
2X-RAY DIFFRACTION2BB0 - 3631 - 343

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