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- PDB-2x4d: Crystal structure of human phospholysine phosphohistidine inorgan... -

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Basic information

Entry
Database: PDB / ID: 2x4d
TitleCrystal structure of human phospholysine phosphohistidine inorganic pyrophosphate phosphatase LHPP
ComponentsPHOSPHOLYSINE PHOSPHOHISTIDINE INORGANIC PYROPHOSPHATE PHOSPHATASE
KeywordsHYDROLASE
Function / homology
Function and homology information


Pyrophosphate hydrolysis / inorganic diphosphatase / inorganic diphosphate phosphatase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / phosphate-containing compound metabolic process / phosphatase activity / nuclear speck / protein homodimerization activity / nucleus / metal ion binding / cytosol
Similarity search - Function
HAD hydrolase, LHPP/HDHD2 / 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
PYROPHOSPHATE 2- / Phospholysine phosphohistidine inorganic pyrophosphate phosphatase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsVollmar, M. / Gileadi, C. / Guo, K. / Savitsky, P. / Muniz, J.R.C. / Yue, W. / Allerston, C. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. ...Vollmar, M. / Gileadi, C. / Guo, K. / Savitsky, P. / Muniz, J.R.C. / Yue, W. / Allerston, C. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Kavanagh, K.L. / Oppermann, U.
CitationJournal: To be Published
Title: Crystal Structure of Human Phospholysine Phosphohistidine Inorganic Pyrophosphate Phosphatase Lhpp
Authors: Vollmar, M. / Gileadi, C. / Guo, K. / Savitsky, P. / Muniz, J.R.C. / Yue, W. / Allerston, C. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Kavanagh, K.L. / Oppermann, U.
History
DepositionJan 29, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 24, 2018Group: Advisory / Database references / Structure summary
Category: audit_author / citation_author / pdbx_unobs_or_zero_occ_atoms
Item: _audit_author.name / _citation_author.name
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.pdbx_dist_value / _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_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_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: PHOSPHOLYSINE PHOSPHOHISTIDINE INORGANIC PYROPHOSPHATE PHOSPHATASE
B: PHOSPHOLYSINE PHOSPHOHISTIDINE INORGANIC PYROPHOSPHATE PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1409
Polymers58,1702
Non-polymers9697
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-28.8 kcal/mol
Surface area19640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.210, 39.410, 112.920
Angle α, β, γ (deg.)90.00, 91.79, 90.00
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
1111A1 - 45
2111B1 - 45
1211A47 - 89
2211B47 - 89
1311A91 - 103
2311B91 - 103
1411A105 - 133
2411B105 - 133
1511A135 - 144
2511B135 - 144
1611A146 - 196
2611B146 - 196
1711A198 - 239
2711B198 - 239
1811A241 - 247
2811B241 - 247
1911A249 - 271
2911B249 - 271

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein PHOSPHOLYSINE PHOSPHOHISTIDINE INORGANIC PYROPHOSPHATE PHOSPHATASE / HLHPP


Mass: 29085.182 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: AS A RESULT OF EXPRESSION SYSTEM SEQUENCE STARTS WITH SER0
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2
References: UniProt: Q9H008, inorganic diphosphatase, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases

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Non-polymers , 5 types, 219 molecules

#2: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 160 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLU 161 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, LYS 160 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLU 161 TO ALA ENGINEERED RESIDUE IN CHAIN B, LYS 160 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 161 TO ALA
Sequence detailsRESIDUES 160 AND 161 ARE MUTATED TO ALA. THE GLN ARG DISCREPANCY IS A KNOW VARIANT.

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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: 2.27 Å3/Da / Density % sol: 45.76 % / Description: NONE
Crystal growDetails: 0.3M NA FORMATE, 25W/V PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.92→31.62 Å / Num. obs: 37847 / % possible obs: 94.4 % / Observed criterion σ(I): 1.7 / Redundancy: 4.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.3
Reflection shellResolution: 1.92→2.03 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 1.7 / % possible all: 68.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0089refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HLT

3hlt


Resolution: 1.92→40 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.916 / SU B: 9.871 / SU ML: 0.134 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1902 5 %RANDOM
Rwork0.227 ---
obs0.229 35942 94.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.97 Å20 Å20.83 Å2
2--1.72 Å20 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 1.92→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3455 0 28 212 3695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223539
X-RAY DIFFRACTIONr_bond_other_d0.0020.022291
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.9794796
X-RAY DIFFRACTIONr_angle_other_deg1.72735603
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0715476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.60524.104134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.5915528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2611520
X-RAY DIFFRACTIONr_chiral_restr0.0870.2546
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214037
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02690
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6131.52381
X-RAY DIFFRACTIONr_mcbond_other0.2721.5993
X-RAY DIFFRACTIONr_mcangle_it0.98423739
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.96331158
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7614.51057
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2330 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.060.05
2Btight positional0.060.05
1Atight thermal0.180.5
2Btight thermal0.180.5
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 92 -
Rwork0.318 1718 -
obs--60.94 %
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)
12.6251-0.49880.34712.4976-1.17972.27290.0116-0.0528-0.2408-0.0498-0.138-0.28650.19020.13910.12640.03310.01090.07350.030.01490.367246.044922.510161.3882
23.36420.5222-0.49751.0118-0.36872.84390.1577-0.7652-0.05130.1777-0.2431-0.04990.03140.12410.08550.0511-0.05560.0550.19110.02450.269839.73726.293376.01
32.5888-0.1332-1.20761.04871.45377.35220.0261-0.9844-0.34550.3993-0.49720.18990.935-1.70570.47110.2661-0.3750.17531.094-0.02910.350613.064518.342592.718
46.7255-0.42051.50832.70950.04155.1056-0.024-1.0011.02890.4045-0.3646-0.1839-0.3788-1.30870.38860.294-0.04230.06851.3765-0.27060.364113.585231.7252107.155
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 79
2X-RAY DIFFRACTION2A80 - 269
3X-RAY DIFFRACTION3B15 - 198
4X-RAY DIFFRACTION4B199 - 260

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