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- PDB-2hx1: Crystal structure of possible sugar phosphatase, HAD superfamily ... -

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Basic information

Entry
Database: PDB / ID: 2hx1
TitleCrystal structure of possible sugar phosphatase, HAD superfamily (ZP_00311070.1) from CYTOPHAGA HUTCHINSONII ATCC 33406 at 2.10 A resolution
ComponentsPredicted sugar phosphatases of the HAD superfamily
KeywordsHYDROLASE / ZP_00311070.1 / possible sugar phosphatase / HAD superfamily / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


phosphatase activity
Similarity search - Function
HAD-superfamily hydrolase, subfamily IIA, hypothetical 3 / HAD-superfamily hydrolase, subfamily IIA / Haloacid dehalogenase-like hydrolase / HAD-hyrolase-like / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Possible sugar phosphatase, HAD superfamily
Similarity search - Component
Biological speciesCytophaga hutchinsonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of possible sugar phosphatase, HAD superfamily (ZP_00311070.1) from CYTOPHAGA HUTCHINSONII ATCC 33406 at 2.10 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
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
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 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: Predicted sugar phosphatases of the HAD superfamily
B: Predicted sugar phosphatases of the HAD superfamily
C: Predicted sugar phosphatases of the HAD superfamily
D: Predicted sugar phosphatases of the HAD superfamily
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,65342
Polymers127,1404
Non-polymers2,51338
Water18,6461035
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17560 Å2
ΔGint-167 kcal/mol
Surface area42870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.624, 119.462, 151.274
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
12C
22D
32C
42D
52C
62D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLYGLYASNASN2AA0 - 531 - 54
211GLYGLYASNASN2BB0 - 531 - 54
321ASPASPASPASP4AA5455
421ASPASPASPASP4BB5455
531ALAALAILEILE2AA55 - 28156 - 282
631ALAALAILEILE2BB55 - 28156 - 282
112GLYGLYSERSER2CC0 - 1071 - 108
212GLYGLYSERSER2DD0 - 1071 - 108
322ALAALAILEILE5CC108 - 129109 - 130
422ALAALAILEILE5DD108 - 129109 - 130
532GLYGLYILEILE2CC130 - 281131 - 282
632GLYGLYILEILE2DD130 - 281131 - 282

NCS ensembles :
ID
1
2

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Predicted sugar phosphatases of the HAD superfamily


Mass: 31785.027 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cytophaga hutchinsonii (bacteria) / Gene: ZP_00311070.1 / Production host: Escherichia coli (E. coli) / References: GenBank: 48856913, UniProt: A0A6N4STH8*PLUS

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Non-polymers , 5 types, 1073 molecules

#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


Mass: 35.453 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1035 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.37 Å3/Da / Density % sol: 47.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7.5
Details: 15.0% Ethanol, 0.2M MgCl2, 0.1M HEPES pH 7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97932, 0.91837, 0.97915
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 18, 2006 / 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
10.979321
20.918371
30.979151
ReflectionResolution: 2.1→29.323 Å / Num. obs: 70192 / % possible obs: 100 % / Redundancy: 3.7 % / Biso Wilson estimate: 20.6 Å2 / Rmerge(I) obs: 0.152 / Rsym value: 0.152 / Net I/σ(I): 4.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.1-2.153.70.6351.21891450870.635100
2.15-2.213.70.5461.41864250160.546100
2.21-2.283.70.51.21806948770.5100
2.28-2.353.70.4451.71754447140.445100
2.35-2.423.70.3941.91714845930.394100
2.42-2.513.70.342.11651444370.34100
2.51-2.63.70.3082.51600442960.308100
2.6-2.713.70.2642.81536141260.264100
2.71-2.833.70.2283.31476439700.228100
2.83-2.973.70.1724.41417638140.172100
2.97-3.133.70.135.61348936290.13100
3.13-3.323.70.116.51270934290.11100
3.32-3.553.70.0936.91192032180.093100
3.55-3.833.70.0828.11130630540.082100
3.83-4.23.70.078.11021227890.07100
4.2-4.73.70.0639.4938525560.063100
4.7-5.423.60.0659.5818622580.065100
5.42-6.643.60.0778.4693019370.077100
6.64-9.393.50.0629532315250.06299.9
9.39-29.323.20.04511.127728650.04596.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0019refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→29.323 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.401 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.236 / ESU R Free: 0.194
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. NCS RESTRAINTS ARE APPLIED SUCH CHAIN A IS VERY SIMILAR TO CHAIN B, CHAIN C SIMILAR TO CHAIN D. THE NCS BREAKS DOWN FOR C108-129/D108- ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. NCS RESTRAINTS ARE APPLIED SUCH CHAIN A IS VERY SIMILAR TO CHAIN B, CHAIN C SIMILAR TO CHAIN D. THE NCS BREAKS DOWN FOR C108-129/D108-129. 3. EACH ACTIVE SITE HAS A MAGNESIUM BOUND. MAGNESIUM IS PRESENT IN THE CYSTALLIZATION SOLUTION. BASED ON DIFFERENCE MAP, THERE APPEARS ANOTHER NON-WATER ENTITY (NEAR THR 52 OG1) FOR EACH MONOMER. THEY ARE TENATIVELY ASSIGNED AS CHLORIDES (21,22,23,24). A HEPES MOLECULE (PRESENT IN CRYSTALLIZATION SOLUTION) IS MODELLED INTO THE ACTIVE SITE. SINCE HEPES IS SIMILAR IN STRUCTURE TO SUBSTRATES OF THIS ENZYME CONTAINING RIBOSE-PHOSPHATE, IT COULD BE AN INHIBITOR. HOWEVER, DUE TO THE POOR DENSITY, THE ASSIGNMENT IS ONLY TENATIVE. 4. 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 0.7 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.234 3531 5 %RANDOM
Rwork0.179 ---
all0.181 ---
obs0.18146 70121 99.92 %-
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: 23.291 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å20 Å2
2--0.53 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.323 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8884 0 138 1035 10057
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0229166
X-RAY DIFFRACTIONr_bond_other_d0.0020.026147
X-RAY DIFFRACTIONr_angle_refined_deg1.4331.98112415
X-RAY DIFFRACTIONr_angle_other_deg0.972315150
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.43351186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.84225.094371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.952151629
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6811535
X-RAY DIFFRACTIONr_chiral_restr0.0820.21451
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210069
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021750
X-RAY DIFFRACTIONr_nbd_refined0.2090.21797
X-RAY DIFFRACTIONr_nbd_other0.1870.26453
X-RAY DIFFRACTIONr_nbtor_refined0.1790.24529
X-RAY DIFFRACTIONr_nbtor_other0.0860.24679
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2791
X-RAY DIFFRACTIONr_metal_ion_refined0.0290.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2460.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.226
X-RAY DIFFRACTIONr_mcbond_it1.83735878
X-RAY DIFFRACTIONr_mcbond_other0.38332356
X-RAY DIFFRACTIONr_mcangle_it2.84259257
X-RAY DIFFRACTIONr_scbond_it5.19483721
X-RAY DIFFRACTIONr_scangle_it7.049113129
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1640TIGHT POSITIONAL0.050.05
1A1905MEDIUM POSITIONAL0.280.5
1A1640TIGHT THERMAL0.170.5
1A1905MEDIUM THERMAL1.012
2C1512TIGHT POSITIONAL0.070.05
2C1898MEDIUM POSITIONAL0.290.5
2C125LOOSE POSITIONAL0.985
2C1512TIGHT THERMAL0.160.5
2C1898MEDIUM THERMAL0.972
2C125LOOSE THERMAL3.9810
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 245 -
Rwork0.233 4828 -
obs-5073 99.74 %

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