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- PDB-10yv: Structure of a putative GH97 from Cellulomonas fimi -

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Basic information

Entry
Database: PDB / ID: 10yv
TitleStructure of a putative GH97 from Cellulomonas fimi
ComponentsPutative GH97 from Cellulomonas fimi
KeywordsUNKNOWN FUNCTION / hypothetical protein
Function / homology: / : / Uncharacterized protein
Function and homology information
Biological speciesCellulomonas fimi (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.15 Å
AuthorsAlmeida, L.R. / Yamashiro, A. / Bernardes, A. / de Mello, B.L.S.P. / Muniz, J.R.C.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq) Brazil
CitationJournal: To Be Published
Title: Structure of a putative GH97 from Cellulomonas fimi (CASP target)
Authors: Almeida, L.R. / Yamashiro, A. / Bernardes, A. / de Mello, B.L.S.P. / Muniz, J.R.C.
History
DepositionFeb 12, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative GH97 from Cellulomonas fimi
B: Putative GH97 from Cellulomonas fimi
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,53827
Polymers57,8382
Non-polymers1,70025
Water12,178676
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-183 kcal/mol
Surface area19850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.424, 74.434, 132.431
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-IDDetails (eV)
d_1ens_1(chain "A" and (resid 42 through 137 or resid 139 through 316))
d_2ens_1(chain "B" and (resid 42 through 137 or resid 139...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ALAALATRPTRPAA42 - 1371 - 96
d_12THRTHRGLYGLYAA139 - 31698 - 275
d_21ALAALATRPTRPBB42 - 1371 - 96
d_22THRTHRGLYGLYBB139 - 31698 - 275

NCS oper: (Code: givenMatrix: (-0.9995014950281, -0.030841282030297, -0.006751056163147), (-0.031565900406732, 0.97217147415411, 0.23213405345302), (-0.00059612758915676, 0.23223143663971, -0. ...NCS oper: (Code: given
Matrix: (-0.9995014950281, -0.030841282030297, -0.006751056163147), (-0.031565900406732, 0.97217147415411, 0.23213405345302), (-0.00059612758915676, 0.23223143663971, -0.97266037467769)
Vector: 90.301430540621, -13.469498649378, 126.43316742059)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Putative GH97 from Cellulomonas fimi


Mass: 28919.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cellulomonas fimi (bacteria) / Gene: Celf_0121 / Production host: Escherichia coli (E. coli) / References: UniProt: F4H4S0

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Non-polymers , 5 types, 701 molecules

#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cd
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 676 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 3.04 Å3/Da / Density % sol: 59.58 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Cadmium chloride hydrate, 0.1 M Sodium acetate trihydrate pH 4.6 and 30% v/v Polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 VENTURE / Wavelength: 1.5418 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Mar 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→66.22 Å / Num. obs: 73531 / % possible obs: 99.18 % / Redundancy: 7.1 % / Biso Wilson estimate: 18.87 Å2 / CC1/2: 0.95 / Net I/σ(I): 2
Reflection shellResolution: 2.15→2.17 Å / Num. unique obs: 1266 / CC1/2: 0.99 / % possible all: 99.84

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Processing

Software
NameVersionClassification
PHENIX2.0_5936refinement
SAINTdata reduction
XSCALEdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→37.97 Å / SU ML: 0.2387 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.8666
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2359 3727 5.07 %
Rwork0.2071 69804 -
obs0.2086 73531 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.09 Å2
Refinement stepCycle: LAST / Resolution: 2.15→37.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4084 0 25 676 4785
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00414210
X-RAY DIFFRACTIONf_angle_d0.63175812
X-RAY DIFFRACTIONf_chiral_restr0.045661
X-RAY DIFFRACTIONf_plane_restr0.0101754
X-RAY DIFFRACTIONf_dihedral_angle_d12.34241366
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.47581696347714 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.180.28941590.26062551X-RAY DIFFRACTION99.85
2.18-2.210.27811160.26812656X-RAY DIFFRACTION100
2.21-2.240.31181510.26182581X-RAY DIFFRACTION99.96
2.24-2.270.28921440.24352622X-RAY DIFFRACTION99.89
2.27-2.30.26511350.25262589X-RAY DIFFRACTION100
2.3-2.340.30681170.24122610X-RAY DIFFRACTION99.96
2.34-2.380.25171400.23372619X-RAY DIFFRACTION99.96
2.38-2.420.27741350.24332583X-RAY DIFFRACTION99.82
2.42-2.460.28741550.2392625X-RAY DIFFRACTION99.78
2.46-2.510.27221270.24052618X-RAY DIFFRACTION100
2.51-2.560.26941330.23582596X-RAY DIFFRACTION99.82
2.56-2.620.29471520.23052554X-RAY DIFFRACTION99.82
2.62-2.680.30281360.23842649X-RAY DIFFRACTION99.82
2.68-2.740.20111540.22292602X-RAY DIFFRACTION99.67
2.74-2.820.26051320.21982573X-RAY DIFFRACTION99.74
2.82-2.90.25291370.22912614X-RAY DIFFRACTION99.85
2.9-2.990.27681340.2192597X-RAY DIFFRACTION99.53
2.99-3.10.30041410.22592612X-RAY DIFFRACTION99.57
3.1-3.220.26961300.21262606X-RAY DIFFRACTION99.24
3.22-3.370.19111360.19612561X-RAY DIFFRACTION98.32
3.37-3.550.27031350.19522542X-RAY DIFFRACTION97.63
3.55-3.770.2221420.18342534X-RAY DIFFRACTION97.88
3.77-4.060.17511300.1692512X-RAY DIFFRACTION96.63
4.06-4.470.16121410.16012526X-RAY DIFFRACTION96.67
4.47-5.110.15191320.14942559X-RAY DIFFRACTION98.03
5.12-6.440.18241390.1712573X-RAY DIFFRACTION98.26
6.44-37.970.21511440.18442540X-RAY DIFFRACTION97.96
Refinement TLS params.Method: refined / Origin x: 44.569 Å / Origin y: 35.543 Å / Origin z: 68.196 Å
111213212223313233
T0.13627345475921 Å20.0012537793927988 Å20.027222962294234 Å2-0.105207803811 Å2-0.0029532408525355 Å2--0.12971118544455 Å2
L0.37652199310583 °2-0.074751531475525 °20.5728445878619 °2-0.22629491886405 °2-0.22477162357109 °2--1.7861274438732 °2
S-0.019857708805965 Å °-0.024423648245535 Å °0.03887 Å °0.022475994204555 Å °0.0044328935514484 Å °-0.0125 Å °-0.11740974201969 Å °-0.048956213703394 Å °0.01155 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 42:316 OR RESID 401:404 OR RESID 405:408 OR RESID 501:849 OR RESID 409:409 OR RESID 410:411 ) ) OR ( CHAIN B AND ( RESID 42:316 OR RESID 401:406 OR RESID 407:410 OR RESID 501:827 OR RESID 411:411 OR RESID 412:414 ) )A42 - 316
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 42:316 OR RESID 401:404 OR RESID 405:408 OR RESID 501:849 OR RESID 409:409 OR RESID 410:411 ) ) OR ( CHAIN B AND ( RESID 42:316 OR RESID 401:406 OR RESID 407:410 OR RESID 501:827 OR RESID 411:411 OR RESID 412:414 ) )A401 - 404
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 42:316 OR RESID 401:404 OR RESID 405:408 OR RESID 501:849 OR RESID 409:409 OR RESID 410:411 ) ) OR ( CHAIN B AND ( RESID 42:316 OR RESID 401:406 OR RESID 407:410 OR RESID 501:827 OR RESID 411:411 OR RESID 412:414 ) )A405 - 408
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 42:316 OR RESID 401:404 OR RESID 405:408 OR RESID 501:849 OR RESID 409:409 OR RESID 410:411 ) ) OR ( CHAIN B AND ( RESID 42:316 OR RESID 401:406 OR RESID 407:410 OR RESID 501:827 OR RESID 411:411 OR RESID 412:414 ) )A501 - 849
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID 42:316 OR RESID 401:404 OR RESID 405:408 OR RESID 501:849 OR RESID 409:409 OR RESID 410:411 ) ) OR ( CHAIN B AND ( RESID 42:316 OR RESID 401:406 OR RESID 407:410 OR RESID 501:827 OR RESID 411:411 OR RESID 412:414 ) )A409
6X-RAY DIFFRACTION1( CHAIN A AND ( RESID 42:316 OR RESID 401:404 OR RESID 405:408 OR RESID 501:849 OR RESID 409:409 OR RESID 410:411 ) ) OR ( CHAIN B AND ( RESID 42:316 OR RESID 401:406 OR RESID 407:410 OR RESID 501:827 OR RESID 411:411 OR RESID 412:414 ) )A410 - 411
7X-RAY DIFFRACTION1( CHAIN A AND ( RESID 42:316 OR RESID 401:404 OR RESID 405:408 OR RESID 501:849 OR RESID 409:409 OR RESID 410:411 ) ) OR ( CHAIN B AND ( RESID 42:316 OR RESID 401:406 OR RESID 407:410 OR RESID 501:827 OR RESID 411:411 OR RESID 412:414 ) )B42 - 316
8X-RAY DIFFRACTION1( CHAIN A AND ( RESID 42:316 OR RESID 401:404 OR RESID 405:408 OR RESID 501:849 OR RESID 409:409 OR RESID 410:411 ) ) OR ( CHAIN B AND ( RESID 42:316 OR RESID 401:406 OR RESID 407:410 OR RESID 501:827 OR RESID 411:411 OR RESID 412:414 ) )B401 - 406
9X-RAY DIFFRACTION1( CHAIN A AND ( RESID 42:316 OR RESID 401:404 OR RESID 405:408 OR RESID 501:849 OR RESID 409:409 OR RESID 410:411 ) ) OR ( CHAIN B AND ( RESID 42:316 OR RESID 401:406 OR RESID 407:410 OR RESID 501:827 OR RESID 411:411 OR RESID 412:414 ) )B407 - 410
10X-RAY DIFFRACTION1( CHAIN A AND ( RESID 42:316 OR RESID 401:404 OR RESID 405:408 OR RESID 501:849 OR RESID 409:409 OR RESID 410:411 ) ) OR ( CHAIN B AND ( RESID 42:316 OR RESID 401:406 OR RESID 407:410 OR RESID 501:827 OR RESID 411:411 OR RESID 412:414 ) )B501 - 827
11X-RAY DIFFRACTION1( CHAIN A AND ( RESID 42:316 OR RESID 401:404 OR RESID 405:408 OR RESID 501:849 OR RESID 409:409 OR RESID 410:411 ) ) OR ( CHAIN B AND ( RESID 42:316 OR RESID 401:406 OR RESID 407:410 OR RESID 501:827 OR RESID 411:411 OR RESID 412:414 ) )B411
12X-RAY DIFFRACTION1( CHAIN A AND ( RESID 42:316 OR RESID 401:404 OR RESID 405:408 OR RESID 501:849 OR RESID 409:409 OR RESID 410:411 ) ) OR ( CHAIN B AND ( RESID 42:316 OR RESID 401:406 OR RESID 407:410 OR RESID 501:827 OR RESID 411:411 OR RESID 412:414 ) )B412 - 414

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