10 20 30 40 50 60 70 80 1YJO - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER PROTEIN BINDING 15-JAN-05 1YJO
TITLE STRUCTURE OF NNQQNY FROM YEAST PRION SUP35 WITH ZINC ACETATE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: EUKARYOTIC PEPTIDE CHAIN RELEASE FACTOR GTP- COMPND 3 BINDING SUBUNIT; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: PRION DETERMINING DOMAIN OF SUP35; COMPND 6 SYNONYM: ERF2, TRANSLATION RELEASE FACTOR 3, ERF3, ERF-3, COMPND 7 OMNIPOTENT SUPPRESSOR PROTEIN 2, G1 TO S PHASE TRANSITION COMPND 8 PROTEIN 1; COMPND 9 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE IS FROM THE PRION DETERMINING SOURCE 4 DOMAIN OF SACCHAROMYCES CEREVISIAE SUP35
KEYWDS KEYWORDS BETA SHEET, STERIC ZIPPER, GLUTAMINE ZIPPER, KEYWDS 2 ASPARAGINE ZIPPER, PROTEIN BINDING
EXPDTA X-RAY DIFFRACTION
AUTHOR R.NELSON,M.R.SAWAYA,M.BALBIRNIE,A.O.MADSEN,C.RIEKEL, AUTHOR 2 R.GROTHE,D.EISENBERG
REVDAT 2 24-FEB-09 1YJO 1 VERSN REVDAT 1 14-JUN-05 1YJO 0
JRNL AUTH R.NELSON,M.R.SAWAYA,M.BALBIRNIE,A.O.MADSEN, JRNL AUTH 2 C.RIEKEL,R.GROTHE,D.EISENBERG JRNL TITL STRUCTURE OF THE CROSS-BETA SPINE OF AMYLOID-LIKE JRNL TITL 2 FIBRILS. JRNL REF NATURE V. 435 773 2005 JRNL REFN ISSN 0028-0836 JRNL PMID 15944695 JRNL DOI 10.1038/NATURE03680
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.54 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 1250 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.103 REMARK 3 R VALUE (WORKING SET) : 0.102 REMARK 3 FREE R VALUE : 0.152 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.000 REMARK 3 FREE R VALUE TEST SET COUNT : 52 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.33 REMARK 3 REFLECTION IN BIN (WORKING SET) : 76 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.10 REMARK 3 BIN R VALUE (WORKING SET) : 0.0120 REMARK 3 BIN FREE R VALUE SET COUNT : 5 REMARK 3 BIN FREE R VALUE : 0.0135 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 55 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 11 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 5.76 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.16000 REMARK 3 B22 (A**2) : -0.44000 REMARK 3 B33 (A**2) : 0.73000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.28000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.043 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.047 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.025 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.463 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.985 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.960 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 58 ; 0.007 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 37 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 77 ; 1.077 ; 1.892 REMARK 3 BOND ANGLES OTHERS (DEGREES): 88 ; 0.728 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 5 ; 8.504 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 6 ;59.937 ;28.333 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 8 ; 9.092 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 6 ; 0.092 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 71 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 9 ; 0.000 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 4 ; 0.225 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 20 ; 0.187 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 18 ; 0.194 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 33 ; 0.083 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 4 ; 0.219 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.039 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 6 ; 0.171 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 13 ; 0.339 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.181 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): 1 ; 0.016 ; 0.200 REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 43 ; 0.663 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 14 ; 0.228 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 49 ; 0.895 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 33 ; 1.394 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 28 ; 1.715 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS
REMARK 4 REMARK 4 1YJO COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JAN-05. REMARK 100 THE RCSB ID CODE IS RCSB031589.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-SEP-04 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID13 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.975 REMARK 200 MONOCHROMATOR : CHANNEL-CUT SI-111 REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : ELLIPSOIDAL MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2166 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 80.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.14600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.42600 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 10.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: ZINC SULFATE, SODIUM ACETATE, REMARK 280 HEPES, PH 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, REMARK 280 PH 7.00
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 2.43500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL
REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). THE SECOND BETA STRAND OF REMARK 300 THE BETA SANDWICH IS GENERATED AS DESCRIBED IN REMARK 350. REMARK 300 BETA SHEETS ARE GENERATED FROM UNIT CELL TRANSLATIONS REMARK 300 ALONG THE UNIT CELL B DIMENSION: X,Y+1,Z.
REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 2.43500 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 7 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 6 O REMARK 620 2 TYR A 6 OXT 50.9 REMARK 620 3 ACY A 10 OXT 112.4 86.6 REMARK 620 4 ASN A 1 N 102.5 153.2 104.3 REMARK 620 5 ACY A 10 O 113.7 85.3 111.0 112.3 REMARK 620 6 ACY A 10 O 118.9 85.6 10.6 109.5 100.3 REMARK 620 N 1 2 3 4 5
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 7 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 10
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YJP RELATED DB: PDB
DBREF 1YJO A 1 6 UNP P05453 ERF2_YEAST 8 13
SEQRES 1 A 6 ASN ASN GLN GLN ASN TYR
HET ZN A 7 1 HET ACY A 10 4
HETNAM ZN ZINC ION HETNAM ACY ACETIC ACID
FORMUL 2 ZN ZN 2+ FORMUL 3 ACY C2 H4 O2 FORMUL 4 HOH *7(H2 O)
LINK ZN ZN A 7 O TYR A 6 1555 1555 2.01 LINK ZN ZN A 7 OXT TYR A 6 1555 1555 2.72 LINK ZN ZN A 7 OXT ACY A 10 1555 1555 1.96 LINK ZN ZN A 7 N ASN A 1 1555 1655 2.12 LINK ZN ZN A 7 O ACY A 10 1555 1545 2.01 LINK ZN ZN A 7 O ACY A 10 1565 1555 2.01
SITE 1 AC1 3 ASN A 1 TYR A 6 ACY A 10 SITE 1 AC2 4 ASN A 1 ASN A 2 TYR A 6 ZN A 7
CRYST1 21.153 4.870 23.130 90.00 102.93 90.00 P 1 21 1 2
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.047275 0.000000 0.010853 0.00000
SCALE2 0.000000 0.205339 0.000000 0.00000
SCALE3 0.000000 0.000000 0.044359 0.00000