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- PDB-4yf1: 1.85 angstrom crystal structure of lmo0812 from Listeria monocyto... -

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Basic information

Entry
Database: PDB / ID: 4yf1
Title1.85 angstrom crystal structure of lmo0812 from Listeria monocytogenes EGD-e
ComponentsLmo0812 protein
KeywordsHYDROLASE / putative pyrophosphohydrolase / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology: / guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity / HD domain / HD domain profile. / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / CITRATE ANION / Lmo0812 protein
Function and homology information
Biological speciesListeria monocytogenes serovar 1/2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsKrishna, S.N. / Light, S.H. / Filippova, E.V. / Minasov, G. / Kiryukhina, O. / Jedrzejczak, R. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To Be Published
Title: 1.85 angstrom crystal structure of lmo0812 from Listeria monocytogenes EGD-e
Authors: Krishna, S.N. / Light, S.H. / Filippova, E.V. / Minasov, G. / Kiryukhina, O. / Jedrzejczak, R. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
History
DepositionFeb 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_entry_details / pdbx_modification_feature / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn / struct_conn_type / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _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_conn_type.id / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lmo0812 protein
B: Lmo0812 protein
C: Lmo0812 protein
D: Lmo0812 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,4237
Polymers88,1884
Non-polymers2353
Water9,152508
1
A: Lmo0812 protein
C: Lmo0812 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1173
Polymers44,0942
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-25 kcal/mol
Surface area15520 Å2
MethodPISA
2
B: Lmo0812 protein
D: Lmo0812 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3064
Polymers44,0942
Non-polymers2122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-23 kcal/mol
Surface area15830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.811, 58.675, 95.730
Angle α, β, γ (deg.)90.00, 114.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Lmo0812 protein


Mass: 22046.979 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (bacteria)
Strain: ATCC BAA-679 / EGD-e / Gene: lmo0812 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Y8T2
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 508 / Source method: isolated from a natural source / Formula: H2O
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: 2.55 Å3/Da / Density % sol: 51.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M tri-sodium citrate, pH 5.5, 20% (w/v) PEG 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 75985 / % possible obs: 99.2 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 31.6
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 2.36 / Num. unique all: 3546 / % possible all: 92.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→29.34 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.954 / SU B: 6.428 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20801 3735 5 %RANDOM
Rwork0.18028 ---
obs0.18164 71643 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.102 Å2
Baniso -1Baniso -2Baniso -3
1-4.4 Å20 Å20.08 Å2
2---2.83 Å2-0 Å2
3----1.16 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4997 0 15 508 5520
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195242
X-RAY DIFFRACTIONr_bond_other_d0.0010.024961
X-RAY DIFFRACTIONr_angle_refined_deg1.381.9497107
X-RAY DIFFRACTIONr_angle_other_deg0.883311413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.6065634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.52624.052269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.37115902
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8351538
X-RAY DIFFRACTIONr_chiral_restr0.0880.2766
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.025947
X-RAY DIFFRACTIONr_gen_planes_other0.0180.021247
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_it1.3362.0662503
X-RAY DIFFRACTIONr_mcbond_other1.3362.0652502
X-RAY DIFFRACTIONr_mcangle_it2.1853.0783133
X-RAY DIFFRACTIONr_mcangle_other2.1853.0793134
X-RAY DIFFRACTIONr_scbond_it1.7792.3422739
X-RAY DIFFRACTIONr_scbond_other1.7762.3412737
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9613.4223969
X-RAY DIFFRACTIONr_long_range_B_refined6.83618.1816476
X-RAY DIFFRACTIONr_long_range_B_other6.49817.2456233
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 262 -
Rwork0.29 4935 -
obs--93.17 %
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)
10.7481-0.5359-0.10823.2446-0.67031.09230.0427-0.02440.0043-0.3783-0.0201-0.0063-0.1138-0.0121-0.02260.10420.0038-0.04080.1282-0.0150.1548-44.66-6.0906-8.5981
24.2721.1446-2.16612.3796-0.07933.88870.26080.25880.04380.0406-0.1484-0.1819-0.244-0.005-0.11240.0270.0207-0.0240.13850.00640.1782-35.25815.54411.659
31.82540.0446-0.08781.8932-0.03721.0137-0.0626-0.0124-0.1354-0.0173-0.0028-0.20150.09310.10790.06540.0197-0.0009-0.02860.13830.00570.222-32.318-6.68714.8556
46.7387-0.3496-0.78582.161-0.34861.34410.1797-0.1941-0.10110.1793-0.1653-0.01960.2368-0.0391-0.01430.0969-0.0372-0.02750.06620.01410.122-38.3279-12.10949.9284
50.6708-0.26930.49672.90660.16541.27010.03560.0118-0.0228-0.3083-0.02010.0250.1645-0.0191-0.01550.0839-0.00920.03850.10520.00840.1223-0.343414.7071-8.6518
61.220800.36413.0659-0.36331.18580.10670.0244-0.0682-0.0645-0.06020.0998-0.0548-0.0046-0.04650.0241-0.00460.01590.1246-0.00310.1277-6.25338.77452.4117
74.9536-0.60081.58761.6651-0.14121.40380.0036-0.08620.23070.0564-0.02030.1623-0.0906-0.12480.01670.0195-0.00380.03310.09270.00540.1124-14.122914.25996.8426
86.4288-0.27380.40581.7873-0.23461.87760.1536-0.01290.1470.2186-0.0866-0.0879-0.19490.0042-0.06710.0648-0.02680.02980.0334-0.01490.0717-5.904220.7610.5521
92.7241.6238-0.06013.0650.34041.4547-0.06420.08670.0583-0.33210.0632-0.1154-0.27170.05680.00090.14580.0197-0.04070.07540.00610.0752-46.6659-11.4168-19.8064
100.6840.52410.39881.1368-1.01042.8125-0.0120.03130.04460.0837-0.0311-0.0658-0.18330.13780.04310.05850.0146-0.01930.1353-0.0020.1375-55.075-11.9894-31.0213
1113.33172.3252-7.09726.5929-3.35312.1312-0.2315-0.28130.1306-0.15180.0745-0.105-0.01310.18470.1570.14170.0142-0.00960.012-0.010.0335-67.3213-2.0184-28.2144
121.4562-0.5068-0.50062.7189-0.08422.71710.13980.0456-0.0506-0.07560.01220.24450.1382-0.1245-0.15190.0283-0.0127-0.02240.1110.01980.0532-63.4484-16.5645-31.3496
132.53331.4101-0.40062.7615-0.90721.791-0.05920.0937-0.1174-0.14650.05780.06570.291-0.07010.00140.12290.00690.0250.0471-0.01970.03461.101120.2-19.7419
140.30020.3814-0.51021.08920.41023.4168-0.01760.0299-0.03460.0485-0.03770.04850.1675-0.12760.05530.0391-0.00290.01380.1141-0.01540.06926.657321.1748-32.6716
153.86040.17150.92760.90570.08656.1888-0.0522-0.2627-0.65980.17760.0558-0.1510.61180.2918-0.00360.2210.0836-0.01390.2060.0030.285722.215510.4625-33.1015
161.734-0.2825-0.19163.03481.30032.50030.15640.05390.0478-0.05520.0377-0.2134-0.05750.1931-0.19410.0213-0.0230.01080.1133-0.02090.029916.053127.0341-33.3446
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 80
2X-RAY DIFFRACTION2A81 - 102
3X-RAY DIFFRACTION3A103 - 158
4X-RAY DIFFRACTION4A159 - 179
5X-RAY DIFFRACTION5B19 - 81
6X-RAY DIFFRACTION6B82 - 121
7X-RAY DIFFRACTION7B122 - 158
8X-RAY DIFFRACTION8B159 - 180
9X-RAY DIFFRACTION9C27 - 82
10X-RAY DIFFRACTION10C83 - 125
11X-RAY DIFFRACTION11C126 - 137
12X-RAY DIFFRACTION12C138 - 180
13X-RAY DIFFRACTION13D27 - 81
14X-RAY DIFFRACTION14D82 - 122
15X-RAY DIFFRACTION15D123 - 140
16X-RAY DIFFRACTION16D141 - 180

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