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- PDB-3fzq: Crystal structure of putative haloacid dehalogenase-like hydrolas... -

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Entry
Database: PDB / ID: 3fzq
TitleCrystal structure of putative haloacid dehalogenase-like hydrolase (YP_001086940.1) from Clostridium difficile 630 at 2.10 A resolution
ComponentsPutative hydrolase
KeywordsHYDROLASE / YP_001086940.1 / putative haloacid dehalogenase-like hydrolase / 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
Similarity search - Function
Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 - #10 / Cof family / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 / HAD-superfamily hydrolase, subfamily IIB / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD-like superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Putative hydrolase, HAD superfamily, subfamily IIB
Similarity search - Component
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative haloacid dehalogenase-like hydrolase (YP_001086940.1) from Clostridium difficile 630 at 2.10 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / 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 / 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_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: Putative hydrolase
B: Putative hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,65913
Polymers63,9492
Non-polymers70911
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.232, 55.737, 116.778
Angle α, β, γ (deg.)90.000, 96.970, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 143
2114B1 - 143
1216A144 - 273
2216B144 - 273
DetailsCRYSTAL PACKING ANALYSIS AND ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUGGEST THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Putative hydrolase /


Mass: 31974.553 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 630 / Gene: CD0467, YP_001086940.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q188R2
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 359 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS 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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.1
Details: NANODROP, 0.20M Na2HPO4, 20.0% PEG 3350, No Buffer pH 9.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91162, 0.97882, 0.97828
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 13, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.978821
30.978281
ReflectionResolution: 2.1→29.828 Å / Num. obs: 36707 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 27.96 Å2 / Rmerge(I) obs: 0.108 / Rsym value: 0.108 / Net I/σ(I): 10.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.1-2.153.60.5032.1983827040.50399.6
2.15-2.213.70.4492.4960926140.44999.8
2.21-2.283.70.3642.9931825250.36499.9
2.28-2.353.70.3453.2922725100.34599.9
2.35-2.423.70.2824896524160.282100
2.42-2.513.70.2534.6861923080.25399.9
2.51-2.63.70.2334.9847122600.233100
2.6-2.713.80.1816.4821521630.181100
2.71-2.833.80.167.6799620860.16100
2.83-2.973.80.1349.3767619950.134100
2.97-3.133.80.1111.9724118850.11100
3.13-3.323.80.09514.9692118080.095100
3.32-3.553.80.08118650017010.081100
3.55-3.833.80.06822597815660.068100
3.83-4.23.80.06325556214570.063100
4.2-4.73.80.05826.4496713150.058100
4.7-5.423.80.05926.4444311820.059100
5.42-6.643.70.06724.236779920.067100
6.64-9.393.60.0727.527987850.07100
9.39-29.8283.20.0732.213784350.0796.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→29.828 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.928 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 9.981 / SU ML: 0.138 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.216 / ESU R Free: 0.18
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN 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 RECORDS CONTAIN 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. TLS GROUPS WERE ASSIGNED WITH THE AID OF TLSMD. 5. NA ION, ETHYLENE GLYCOL AND PHOSPHATE MOLECULES FROM THE CRYSTALLIZATION/CRYO SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1833 5 %RANDOM
Rwork0.188 ---
obs0.19 36695 99.79 %-
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 max: 74.57 Å2 / Biso mean: 33.703 Å2 / Biso min: 15.72 Å2
Baniso -1Baniso -2Baniso -3
1-3.82 Å20 Å2-0.31 Å2
2---0.3 Å20 Å2
3----3.59 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.828 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4217 0 43 359 4619
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224356
X-RAY DIFFRACTIONr_bond_other_d0.0030.022965
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.9595852
X-RAY DIFFRACTIONr_angle_other_deg1.34837271
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2285542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.34825.616219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.6715839
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4211521
X-RAY DIFFRACTIONr_chiral_restr0.0920.2653
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024829
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02826
X-RAY DIFFRACTIONr_nbd_refined0.1620.2891
X-RAY DIFFRACTIONr_nbd_other0.140.23311
X-RAY DIFFRACTIONr_nbtor_refined0.1530.22127
X-RAY DIFFRACTIONr_nbtor_other0.0730.22206
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2356
X-RAY DIFFRACTIONr_metal_ion_refined0.1560.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0810.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1040.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0750.26
X-RAY DIFFRACTIONr_mcbond_it0.98622642
X-RAY DIFFRACTIONr_mcbond_other0.18521094
X-RAY DIFFRACTIONr_mcangle_it1.83744265
X-RAY DIFFRACTIONr_scbond_it2.37141746
X-RAY DIFFRACTIONr_scangle_it3.47361580
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
1648MEDIUM POSITIONAL0.20.5
1701LOOSE POSITIONAL0.325
1648MEDIUM THERMAL0.632
1701LOOSE THERMAL2.4210
LS refinement shellResolution: 2.1→2.16 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 136 -
Rwork0.238 2536 -
all-2672 -
obs--98.45 %
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)
10.74890.05350.89570.8939-0.75872.43880.0205-0.1259-0.04750.15420.03450.06340.1343-0.1906-0.055-0.06150.0120.03420.04180.04150.004532.59463.002545.4517
20.37990.05180.9960.63010.73783.1931-0.09420.02190.03860.02770.1091-0.0162-0.43960.3008-0.01480.0077-0.0636-0.00220.0263-0.0007-0.01242.325423.928437.7616
32.7972-0.14755.608719.80611.395511.39080.22320.25880.4914-0.62820.2069-0.9656-1.53130.3061-0.43020.0067-0.054-0.0226-0.1072-0.0541-0.082843.497614.621247.2763
40.41650.3730.27071.1895-0.35081.9978-0.1082-0.1210.05820.10470.08540.1581-0.4147-0.17970.0228-0.03220.05850.00910.0069-0.0059-0.01231.248521.23740.8122
51.1707-0.68421.06012.4880.01992.7988-0.1166-0.4776-0.05810.36970.20640.1994-0.2033-0.4732-0.08980.00250.06870.08610.14740.0537-0.035227.26427.690658.6798
60.2345-0.3973-0.05540.8684-0.59272.4268-0.0397-0.0721-0.00380.0086-0.02150.0232-0.31910.15570.0613-0.0707-0.0349-0.0116-0.03250.0150.000435.789821.41339.404
70.2253-0.3663-0.64790.76910.80582.2174-0.0112-0.19120.04160.00450.0815-0.08480.22840.2574-0.0703-0.10590.03580.003-0.00230.03430.014344.710.164721.5713
80.7251-0.5656-0.12390.90220.17911.43930.00020.0091-0.1089-0.0104-0.00940.06040.20260.11380.0091-0.08590.01340.0161-0.03540.00790.029939.4138-2.503317.7467
91.6411-1.08530.10291.9376-1.07121.8715-0.0421-0.0845-0.0447-0.06730.10580.19820.0657-0.1649-0.0637-0.1287-0.0065-0.0209-0.0261-0.01020.026826.492813.01918.198
100.5424-0.3452-0.75381.1427-0.05712.62950.01750.0867-0.0466-0.1721-0.07160.0344-0.05490.05870.0541-0.06680.0131-0.0261-0.03570.0068-0.005234.421916.2935-4.1072
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 78
2X-RAY DIFFRACTION2A79 - 134
3X-RAY DIFFRACTION3A135 - 141
4X-RAY DIFFRACTION4A142 - 229
5X-RAY DIFFRACTION5A230 - 273
6X-RAY DIFFRACTION6B1 - 78
7X-RAY DIFFRACTION7B79 - 127
8X-RAY DIFFRACTION8B143 - 198
9X-RAY DIFFRACTION9B199 - 229
10X-RAY DIFFRACTION10B230 - 273

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