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- PDB-6dzd: Crystal structure of Bacillus licheniformis hypothetical protein YfiH -

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Basic information

Entry
Database: PDB / ID: 6dzd
TitleCrystal structure of Bacillus licheniformis hypothetical protein YfiH
Componentshypothetical protein YfiH
KeywordsUNKNOWN FUNCTION / Putative protein / Bacillus licheniformis
Function / homology
Function and homology information


adenosine deaminase activity / S-methyl-5-thioadenosine phosphorylase activity / metal ion binding
Similarity search - Function
CNF1/YfiH-like putative cysteine hydrolases / CNF1/YfiH-like putative cysteine hydrolases / Multi-copper polyphenol oxidoreductase / Multi-copper polyphenol oxidoreductase superfamily / Multi-copper polyphenol oxidoreductase laccase / Cytotoxic necrotizing factor-like, catalytic / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsAlmeida, L.R. / Grejo, M.P. / Mulinari, E.J. / Santos, J.C. / Camargo, S. / Bernardes, A. / Muniz, J.R.C.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2017/16291-5 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)309767/2015-6 Brazil
CitationJournal: To Be Published
Title: Crystal structure of Bacillus licheniformis hypothetical protein YfiH
Authors: Almeida, L.R. / Grejo, M.P. / Mulinari, E.J. / Santos, J.C. / Camargo, S. / Bernardes, A. / Muniz, J.R.C.
History
DepositionJul 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein YfiH
B: hypothetical protein YfiH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7817
Polymers62,5532
Non-polymers2285
Water3,117173
1
A: hypothetical protein YfiH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4164
Polymers31,2761
Non-polymers1403
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: hypothetical protein YfiH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3653
Polymers31,2761
Non-polymers882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.567, 69.464, 179.589
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRTRPTRP(chain 'A' and (resid 4 through 58 or resid 60...AA4 - 204 - 20
12GLNGLNASPASP(chain 'A' and (resid 4 through 58 or resid 60...AA29 - 5729 - 57
13GLNGLNLEULEU(chain 'A' and (resid 4 through 58 or resid 60...AA60 - 27660 - 276
24TYRTYRTRPTRP(chain 'B' and (resid 4 through 18 or (resid 19...BB4 - 204 - 20
25GLNGLNASPASP(chain 'B' and (resid 4 through 18 or (resid 19...BB29 - 5729 - 57
26GLNGLNLEULEU(chain 'B' and (resid 4 through 18 or (resid 19...BB60 - 27660 - 276

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein hypothetical protein YfiH


Mass: 31276.385 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A5A677

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Non-polymers , 5 types, 178 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.2 Å3/Da / Density % sol: 44.1 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / pH: 8.5
Details: 200 mM calcium chloride, 100 mM Tris-HCl pH 8.5 and 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Aug 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.66→54.94 Å / Num. obs: 16046 / % possible obs: 99.9 % / Observed criterion σ(F): 1.5 / Redundancy: 5.9 % / Biso Wilson estimate: 21.76 Å2 / CC1/2: 0.951 / Rmerge(I) obs: 0.247 / Rpim(I) all: 0.163 / Rrim(I) all: 0.297 / Net I/σ(I): 4.5
Reflection shellResolution: 2.66→2.79 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2073 / CC1/2: 0.705 / Rpim(I) all: 0.441 / Rrim(I) all: 0.727 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
SAINTdata reduction
Aimless0.5.32data scaling
PHASER2.5.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T8H

1t8h


Resolution: 2.66→54.94 Å / SU ML: 0.3382 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.9589
RfactorNum. reflection% reflection
Rfree0.2478 778 4.86 %
Rwork0.2144 --
obs0.2161 15993 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.13 Å2
Refinement stepCycle: LAST / Resolution: 2.66→54.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4173 0 5 173 4351
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00794274
X-RAY DIFFRACTIONf_angle_d1.01655797
X-RAY DIFFRACTIONf_chiral_restr0.0527641
X-RAY DIFFRACTIONf_plane_restr0.0073757
X-RAY DIFFRACTIONf_dihedral_angle_d10.30413016
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-2.830.32621380.25432466X-RAY DIFFRACTION99.96
2.83-3.040.30141190.25392500X-RAY DIFFRACTION99.96
3.04-3.350.28231140.24182501X-RAY DIFFRACTION100
3.35-3.840.24531220.19492548X-RAY DIFFRACTION100
3.84-4.830.18791400.16332536X-RAY DIFFRACTION100
4.83-54.950.24181450.23122664X-RAY DIFFRACTION99.22
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)
13.172414721332.222499486561.436692622653.5017241102-2.050157249486.631926095930.309167475765-0.02490607707440.563209472870.67105212808-0.4225598762440.49950633319-1.13415229406-0.2559468429470.4322094866360.3462779139930.106056200478-0.063824054330.457946462354-0.1685273630290.44875151483910.916285786421.155558772937.8699232621
21.28787486573-0.2303600877771.236874714461.897634720411.011685573223.140587563610.0465862605701-0.168788085243-0.141801448110.185097693369-0.1188111577250.1352041585910.330116791492-0.299792455140.04546318613430.107252130247-0.06653824587730.04180715600760.190078083634-0.001135225177880.16192878363617.70186656635.9570173994137.0277965253
34.23440731238-1.13930959181-0.5937516326993.06842331937-0.6272756834561.395928173250.1854753990611.009231231290.0765931219575-0.7341442833860.00160920838799-0.01282485798640.223064861202-0.318087605861-0.1894517330980.265885822932-0.0551449740796-0.04342331613160.3027165123340.001557143513420.17827939867331.962617240217.552001287819.1360089939
42.171334360630.5935725018350.01106493651772.325164503080.7793140941293.60341551777-0.1786208786340.06097281474530.420125130033-0.207311234106-0.0340838442739-0.0936473750803-0.3097180941570.02530929793620.1911650410830.1664563569870.046991178087-0.02648530570250.1618425292380.01333202712880.18033025743320.886975979316.949854528831.1177326556
54.526763159530.8905608054230.2548281772816.38964439441.490508363166.10900878367-0.1167399895550.17429245586-0.467671183457-0.101085129382-0.174361652874-1.612697867150.4305244084671.007160338870.2373691346810.3222624702670.06270011606390.1128946506510.4326474217350.06000670700760.41002292327653.010408905340.470357467522.9976290157
62.153983075340.1118089781211.449454308442.431659366760.4559190691052.95448016559-0.0645221541089-0.1036665275060.250613637958-0.057478993055-0.009404357604120.0286148589604-0.2383193308180.1715326687750.07292522000580.1148529465-0.01417733522570.004806829708780.127396698845-0.007454330697360.16134062779543.214799641355.103103832518.233593614
71.580574422320.326586441582-0.3624975207670.91832686208-0.6216820543930.4676681846430.01693499741250.290146151435-0.025349872227-0.2062881079470.04267331665770.08779925705750.177988845385-0.0821661757068-0.06603940104160.220186031145-0.060139424824-0.05342657736740.228446323053-0.01414387020250.20399930370543.73411157741.08819312837.54502139295
82.736363693931.34399484778-0.3315818483032.24485638121-1.578750834061.68726120959-0.07650278322030.6526612996210.0971058164651-0.452828728290.1007728422060.3835388279180.770525728839-0.229245426658-0.1366879848050.406325530182-0.127575131338-0.1228931034520.4336668025280.114067924120.36802891629126.455488466129.964304331810.8844362498
91.34305210324-0.0965959321175-0.1837810270061.62210581763-0.7181649420752.74963360778-0.0197550074091-0.185824344103-0.154540671028-0.1769013968620.02841928512920.08334036476880.121690516979-0.14309958237-0.05195893983950.169921030771-0.00931644108737-0.0633036579330.1194586890830.003960156017240.18103105564338.778476193837.888466938818.5355393703
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 2:21)
2X-RAY DIFFRACTION2(chain A and resseq 29:183)
3X-RAY DIFFRACTION3(chain A and resseq 184:225)
4X-RAY DIFFRACTION4(chain A and resseq 226:277)
5X-RAY DIFFRACTION5(chain B and resseq 4:21)
6X-RAY DIFFRACTION6(chain B and resseq 29:130)
7X-RAY DIFFRACTION7(chain B and resseq 131:190)
8X-RAY DIFFRACTION8(chain B and resseq 191:218)
9X-RAY DIFFRACTION9(chain B and resseq 219:277)

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