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- PDB-3c37: X-ray structure of the putative Zn-dependent peptidase Q74D82 at ... -

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Basic information

Entry
Database: PDB / ID: 3c37
TitleX-ray structure of the putative Zn-dependent peptidase Q74D82 at the resolution 1.7 A. Northeast Structural Genomics Consortium target GsR143A
ComponentsPeptidase, M48 family
KeywordsHYDROLASE / Q74D82 / GsR143A / Peptidase / M48 family / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Metalloprotease / Protease
Function / homology
Function and homology information


proteolysis involved in protein catabolic process / metalloendopeptidase activity / metal ion binding / membrane
Similarity search - Function
: / Peptidase M48 / Peptidase family M48 / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Peptidase lipoprotein, M48 family
Similarity search - Component
Biological speciesGeobacter sulfurreducens PCA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsKuzin, A.P. / Chen, Y. / Seetharaman, J. / Vorobiev, S.M. / Forouhar, F. / Wang, D. / Mao, L. / Maglaqui, M. / Xiao, R. / Liu, J. ...Kuzin, A.P. / Chen, Y. / Seetharaman, J. / Vorobiev, S.M. / Forouhar, F. / Wang, D. / Mao, L. / Maglaqui, M. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: X-ray structure of the putative Zn-dependent peptidase Q74D82 at the resolution 1.7 A.
Authors: Kuzin, A.P. / Chen, Y. / Seetharaman, J. / Vorobiev, S.M. / Forouhar, F. / Wang, D. / Mao, L. / Maglaqui, M. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionJan 27, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type / 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_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_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: Peptidase, M48 family
B: Peptidase, M48 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1566
Polymers57,8132
Non-polymers3434
Water4,468248
1
A: Peptidase, M48 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0783
Polymers28,9061
Non-polymers1722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peptidase, M48 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0783
Polymers28,9061
Non-polymers1722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.840, 44.613, 71.772
Angle α, β, γ (deg.)88.07, 75.18, 65.64
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Peptidase, M48 family


Mass: 28906.326 Da / Num. of mol.: 2 / Fragment: Residues 21-264
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens PCA (bacteria)
Species: Geobacter sulfurreducens / Strain: PCA / DSM 12127 / Gene: GSU1437 / Production host: Escherichia coli (E. coli) / References: UniProt: Q74D82
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.791 Å3/Da / Density % sol: 31.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Ammonium thiocyanate, 0.1M Sodium citrate, 40% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X4C10.979
SYNCHROTRONAPS 23-ID-D20.979
Detector
TypeIDDetectorDate
MAR CCD 165 mm1CCDNov 11, 2007
ADSC QUANTUM 3152CCDDec 14, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 84304 / % possible obs: 94.7 % / Observed criterion σ(I): -3 / Redundancy: 1.92 % / Rsym value: 0.024 / Net I/σ(I): 30.2
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 1.93 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.167 / % possible all: 86.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→27.43 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.917 / SU B: 2.544 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: The Friedel pairs were used in phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.25386 2160 5 %RANDOM
Rwork0.21928 ---
obs0.22106 40662 100 %-
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: 25.071 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.7→27.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3522 0 16 248 3786
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223635
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2381.9664869
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2475439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.55524.696181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38915665
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0261522
X-RAY DIFFRACTIONr_chiral_restr0.0890.2531
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022724
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.21703
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22521
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2229
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.286
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it11.52253
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.41723528
X-RAY DIFFRACTIONr_scbond_it2.32831516
X-RAY DIFFRACTIONr_scangle_it3.4494.51341
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 129 -
Rwork0.262 2786 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 18.189 Å / Origin y: 7.005 Å / Origin z: 18.244 Å
111213212223313233
T0.0358 Å20.0087 Å20.0227 Å2-0.0405 Å20.0044 Å2--0.0523 Å2
L0.5387 °20.1036 °20.799 °2-0.0761 °20.1529 °2--1.1849 °2
S-0.0169 Å °0.0706 Å °-0.0083 Å °-0.0062 Å °0.011 Å °-0.0276 Å °-0.0131 Å °0.1173 Å °0.0058 Å °

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