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- PDB-2go7: CRYSTAL STRUCTURE OF A HYDROLASE FROM HALOACID DEHALOGENASE-LIKE ... -

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Entry
Database: PDB / ID: 2go7
TitleCRYSTAL STRUCTURE OF A HYDROLASE FROM HALOACID DEHALOGENASE-LIKE FAMILY (SP_2064) FROM STREPTOCOCCUS PNEUMONIAE TIGR4 AT 2.10 A RESOLUTION
Componentshydrolase, haloacid dehalogenase-like family
KeywordsHYDROLASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


hydrolase activity / metal ion binding
Similarity search - Function
Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold ...Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Hydrolase, haloacid dehalogenase-like family / Hydrolase, haloacid dehalogenase-like family
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of (np_346487.1) from Streptococcus pneumoniae TIGR4 at 2.10 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 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 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_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1,2,3,4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ...BIOMOLECULE: 1,2,3,4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY DATA SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hydrolase, haloacid dehalogenase-like family
B: hydrolase, haloacid dehalogenase-like family
C: hydrolase, haloacid dehalogenase-like family
D: hydrolase, haloacid dehalogenase-like family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,24222
Polymers94,6484
Non-polymers59418
Water8,863492
1
A: hydrolase, haloacid dehalogenase-like family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8647
Polymers23,6621
Non-polymers2026
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: hydrolase, haloacid dehalogenase-like family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7574
Polymers23,6621
Non-polymers953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: hydrolase, haloacid dehalogenase-like family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8286
Polymers23,6621
Non-polymers1665
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: hydrolase, haloacid dehalogenase-like family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7935
Polymers23,6621
Non-polymers1314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
A: hydrolase, haloacid dehalogenase-like family
B: hydrolase, haloacid dehalogenase-like family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,62111
Polymers47,3242
Non-polymers2979
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-104 kcal/mol
Surface area18290 Å2
MethodPISA
6
C: hydrolase, haloacid dehalogenase-like family
D: hydrolase, haloacid dehalogenase-like family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,62111
Polymers47,3242
Non-polymers2979
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-103 kcal/mol
Surface area18250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.000, 155.000, 88.440
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: THR / End label comp-ID: GLU / Refine code: 4 / Auth seq-ID: 4 - 204 / Label seq-ID: 5 - 205

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
DetailsSIZE EXCLUSION CHROMATOGRAPHY DATA SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE

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Components

#1: Protein
hydrolase, haloacid dehalogenase-like family /


Mass: 23662.080 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: np_346487.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97NG6, UniProt: A0A0H2URV7*PLUS
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 492 / 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: 3.12 Å3/Da / Density % sol: 60.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 5.5
Details: 0.2M MgCl2, 40.0% PEG-400, 0.1M Citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979224, 0.918370, 0.978940
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 19, 2005 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9792241
20.918371
30.978941
ReflectionResolution: 2.1→29.48 Å / Num. obs: 70459 / % possible obs: 99.3 % / Redundancy: 3.76 % / Biso Wilson estimate: 35.139 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 6.83
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.1-2.170.5211.55205341065496.2
2.17-2.260.3692.3247651278988.2
2.26-2.360.312.7235341213589.6
2.36-2.490.2433.4259621335092.1
2.49-2.640.2034244311262893.6
2.64-2.850.1445.4264491359994.7
2.85-3.130.0898.1256421326097
3.13-3.590.05511.7268771390798.4
3.590.05313.4262011369999.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
XSCALEdata scaling
PDB_EXTRACT1.701data extraction
XDSdata reduction
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→29.29 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 7.502 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.156 / ESU R Free: 0.145
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 ...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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. (3) THERE IS UNKNOWN DENSITY NEAR TYR18 IN CHAINS B AND C, WHICH IS ABSENT FROM CHAINS A AND D. THIS WAS LEFT UNMODELED. SINCE THE UNKNOWN DENSITY IS LOCATED NEAR THE ACTIVE SITE OF THE PROTEIN, THIS COULD BE POSSIBLE TO BE A SUBSTRATE MOLECULE, SUCH AS HALOACID. (4) ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.209 3555 5 %RANDOM
Rwork0.171 ---
obs0.173 70427 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.966 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å2-0.13 Å20 Å2
2---0.27 Å20 Å2
3---0.4 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6478 0 18 492 6988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0226645
X-RAY DIFFRACTIONr_bond_other_d0.0010.024368
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.9469022
X-RAY DIFFRACTIONr_angle_other_deg0.958310648
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0965820
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.98425.029344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.564151113
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8351534
X-RAY DIFFRACTIONr_chiral_restr0.0870.21016
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027501
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021392
X-RAY DIFFRACTIONr_nbd_refined0.2110.21374
X-RAY DIFFRACTIONr_nbd_other0.1840.24547
X-RAY DIFFRACTIONr_nbtor_refined0.1830.23286
X-RAY DIFFRACTIONr_nbtor_other0.0890.23257
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2387
X-RAY DIFFRACTIONr_metal_ion_refined0.0870.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2530.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2570.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1120.213
X-RAY DIFFRACTIONr_mcbond_it1.90534245
X-RAY DIFFRACTIONr_mcbond_other0.68531654
X-RAY DIFFRACTIONr_mcangle_it2.66556545
X-RAY DIFFRACTIONr_scbond_it4.55982833
X-RAY DIFFRACTIONr_scangle_it6.427112472
Refine LS restraints NCS

Ens-ID: 1 / Number: 2568 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.480.5
2BMEDIUM POSITIONAL0.510.5
3CMEDIUM POSITIONAL0.550.5
4DMEDIUM POSITIONAL0.410.5
1AMEDIUM THERMAL1.142
2BMEDIUM THERMAL1.252
3CMEDIUM THERMAL1.192
4DMEDIUM THERMAL0.992
LS refinement shellResolution: 2.099→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 257 -
Rwork0.221 4820 -
obs-5077 97.88 %
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)
11.85790.4976-0.3661.6614-0.09140.94280.0220.14560.3638-0.06980.02380.1207-0.1341-0.1147-0.0458-0.0582-0.0107-0.0042-0.13020.0452-0.085987.98514.412.147
21.6393-0.4829-0.1282.31910.22230.86810.0356-0.02710.1904-0.049-0.0013-0.4283-0.06480.1655-0.0344-0.065-0.04640.0008-0.10920.012-0.0054113.7161-0.092313.2457
31.683-0.4913-0.43271.7556-0.03871.1877-0.0188-0.0144-0.2-0.01720.0573-0.04390.06330.0048-0.0384-0.09360.01-0.0375-0.13150.0354-0.064106.5618-27.122616.8918
42.2681-0.7943-0.46111.07940.31010.8885-0.196-0.3144-0.11330.2670.09350.07830.0879-0.01970.1025-0.00980.00060.0152-0.07940.033-0.130587.8593-17.068530.9728
52.1266-0.0997-0.03221.40220.09511.6523-0.04540.3065-0.5371-0.0986-0.06610.05330.2839-0.01350.1115-0.036-0.05630.0214-0.0167-0.09510.023973.0233-30.86188.4993
64.26281.2178-0.49811.066-0.0581.27740.07-0.08550.01270.0906-0.04360.12-0.0694-0.177-0.0264-0.0974-0.0274-0.0086-0.09380.006-0.083963.1533-11.045921.244
71.99760.3673-0.74581.29140.05243.0466-0.01260.3985-0.0339-0.10830.0350.31030.0694-0.491-0.0224-0.0756-0.0192-0.0440.1182-0.00950.015537.9251-22.317415.3858
83.3327-1.3856-0.40092.27650.6664.0154-0.08710.2326-0.1974-0.20770.19540.04460.0984-0.4025-0.10830.0495-0.1243-0.0610.2415-0.0787-0.03749.4935-28.1759-6.8765
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA3 - 164 - 17
21AA84 - 20685 - 207
32AA17 - 8318 - 84
43BB3 - 164 - 17
53BB84 - 20485 - 205
64BB17 - 8318 - 84
75CC0 - 161 - 17
85CC84 - 20485 - 205
96CC17 - 8318 - 84
107DD3 - 164 - 17
117DD84 - 20585 - 206
128DD17 - 8318 - 84

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