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- PDB-2h1j: 3.1 A X-ray structure of putative Oligoendopeptidase F: Crystals ... -

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Basic information

Entry
Database: PDB / ID: 2h1j
Title3.1 A X-ray structure of putative Oligoendopeptidase F: Crystals grown by microfluidic seeding
ComponentsOligoendopeptidase F
KeywordsHYDROLASE / Structural Genomics / microfluidic seeding / PSI-2 / Protein Structure Initiative / ACCELERATED TECHNOLOGIES CENTER FOR GENE TO 3D STRUCTURE / ATCG3D
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Peptidase M3B, oligoendopeptidase-related / Neurolysin; domain 3 - #30 / Peptidase M3A/M3B catalytic domain / Peptidase family M3 / Peptidase M3A/M3B / Neurolysin; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Oligoendopeptidase F
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å
AuthorsGerdts, C.J. / Tereshko, V. / Dementieva, I. / Collart, F. / Joachimiak, A. / Kossiakoff, A. / Ismagilov, R.F. / Accelerated Technologies Center for Gene to 3D Structure (ATCG3D)
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2006
Title: Time-Controlled Microfluidic Seeding in nL-Volume Droplets To Separate Nucleation and Growth Stages of Protein Crystallization.
Authors: Gerdts, C.J. / Tereshko, V. / Yadav, M.K. / Dementieva, I. / Collart, F. / Joachimiak, A. / Stevens, R.C. / Kuhn, P. / Kossiakoff, A. / Ismagilov, R.F.
History
DepositionMay 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ncs_dom_lim / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ...BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). EACH CHAIN REPRESENTS ONE BIOLOGICAL UNIT. THE OLIGOMERIZATION IS UNKNOWN.
Remark 999At the time of processing, the sequence of this protein is not available at the UNP sequence ...At the time of processing, the sequence of this protein is not available at the UNP sequence database. Residues -2 to 0 are cloning artifacts.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Oligoendopeptidase F
B: Oligoendopeptidase F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,1204
Polymers133,9902
Non-polymers1312
Water362
1
A: Oligoendopeptidase F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0602
Polymers66,9951
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Oligoendopeptidase F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0602
Polymers66,9951
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.324, 119.324, 248.736
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B
151A
161B
171A
181B

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSPHEPHEAA2 - 275 - 30
21LYSLYSPHEPHEBB2 - 275 - 30
32GLYGLYLEULEUAA31 - 3534 - 38
42GLYGLYLEULEUBB31 - 3534 - 38
53ILEILETYRTYRAA43 - 9146 - 94
63ILEILETYRTYRBB43 - 9146 - 94
74LYSLYSGLYGLYAA110 - 211113 - 214
84LYSLYSGLYGLYBB110 - 211113 - 214
95PHEPHEALAALAAA215 - 319218 - 322
105PHEPHEALAALABB215 - 319218 - 322
116LYSLYSASNASNAA323 - 376326 - 379
126LYSLYSASNASNBB323 - 376326 - 379
137PROPROILEILEAA378 - 480381 - 483
147PROPROILEILEBB378 - 480381 - 483
158TYRTYRASPASPAA481 - 489484 - 492
168TYRTYRASPASPBB481 - 489484 - 492
179TYRTYRLEULEUAA490 - 564493 - 567
189TYRTYRLEULEUBB490 - 564493 - 567
DetailsThis entry contains the crystallographic asymmetic unit which consists of 2 chain(s). Each chain represents one biological unit. The oligomerization is unknown.

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Components

#1: Protein Oligoendopeptidase F


Mass: 66994.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: GK0963 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5L1D2*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.83 Å3/Da / Density % sol: 67.87 %
Crystal growTemperature: 296 K / pH: 7
Details: PRECIPITATION FROM A HANGING DROP VAPOR DIFFUSION TRIAL (60% TASCIMATE IN BIS-TRIS PROPANE PH= 7.0) WAS USED TO SEED INTO A 45% TASCIMATE SOLUTION USING A MICROFLUIDIC MICROBATCH SEEDING ...Details: PRECIPITATION FROM A HANGING DROP VAPOR DIFFUSION TRIAL (60% TASCIMATE IN BIS-TRIS PROPANE PH= 7.0) WAS USED TO SEED INTO A 45% TASCIMATE SOLUTION USING A MICROFLUIDIC MICROBATCH SEEDING TECHNIQUE. CONCENTRATION OF PROTEIN WAS 17 MG/ML., TEMPERATURE 296K , pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9793
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 1, 2006 / Details: ADJUSTABLE FOCUSING MIRRORS. K-B GEOMETRY
RadiationMonochromator: DOUBLE CRYSTAL SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 37927 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 9.28
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 1.88 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 3.1→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.927 / SU B: 34.316 / SU ML: 0.263 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.363 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. WE HAVE DETECTED THE DIFFERENCE ELECTRON DENSITY AT >2.0 SIGMA LEVEL IN THE CENTER GROOVE OF THE MOLECULE. WE HAVE USED TASCIMATE (THE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. WE HAVE DETECTED THE DIFFERENCE ELECTRON DENSITY AT >2.0 SIGMA LEVEL IN THE CENTER GROOVE OF THE MOLECULE. WE HAVE USED TASCIMATE (THE HAMPTON RESEARCH PROPRIETARY MIXTURE OF ORGANIC ACIDS) FOR CRYSTALLIZATION. IT IS LIKELY THAT ONE OF THE ORGANIC ACIDS OR THEIR MIXTURE ENTERS THE GROOVE IN THE SOLUTION AND HELPS TO STABILIZE THE CLOSED CONFORMATION OF OLIGOENDOPEPTIDASE F IN THE CRYSTAL FORM. WE DID NOT ATTEMPT TO INTERPRET THE DIFFERENCE DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.22529 1892 5 %RANDOM
Rwork0.18735 ---
obs0.18923 35830 99.96 %-
all-31069 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20.43 Å20 Å2
2--0.86 Å20 Å2
3----1.29 Å2
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9337 0 2 2 9341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.029601
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1311.87912979
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.21351127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.29123.333534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.015151590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9021582
X-RAY DIFFRACTIONr_chiral_restr0.0790.21313
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027592
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2320.24607
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3240.26628
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2234
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2981.55739
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.43929045
X-RAY DIFFRACTIONr_scbond_it0.77534394
X-RAY DIFFRACTIONr_scangle_it1.1334.53934
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
2112tight positional0.030.05
2245medium positional0.290.5
2112tight thermal0.040.5
2245medium thermal0.262
LS refinement shellResolution: 3.1→3.182 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 151 -
Rwork0.293 2547 -
obs--99.78 %
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)
11.32480.29410.46680.97110.11031.2241-0.01390.0570.23850.0342-0.107-0.0312-0.3508-0.14460.1209-0.04740.09720.0498-0.1992-0.0332-0.098341.184432.1445103.8196
20.679-0.40180.26061.7648-0.53850.96140.0605-0.105-0.11070.0994-0.04210.14720.1163-0.2816-0.0184-0.1839-0.1190.0591-0.0592-0.0465-0.149991.51483.4823111.4293
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 564
2X-RAY DIFFRACTION1A601
3X-RAY DIFFRACTION1A602
4X-RAY DIFFRACTION2B1 - 564
5X-RAY DIFFRACTION2B701
6X-RAY DIFFRACTION2B702

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