HEADER SIGNALING PROTEIN 23-APR-13 3WA4
TITLE GRB2 SH2 DOMAIN/CD28-DERIVED PEPTIDE COMPLEX
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: SH2 DOMAIN, UNP RESIDEUS 57-152;
COMPND 5 SYNONYM: ADAPTER PROTEIN GRB2, PROTEIN ASH, SH2/SH3 ADAPTER GRB2;
COMPND 6 ENGINEERED: YES;
COMPND 7 MOL_ID: 2;
COMPND 8 MOLECULE: T-CELL-SPECIFIC SURFACE GLYCOPROTEIN CD28;
COMPND 9 CHAIN: B;
COMPND 10 FRAGMENT: FRAGMENT PEPTIDE, UNP RESIDUES 190-195;
COMPND 11 SYNONYM: TP44;
COMPND 12 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: GRB2, ASH;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 MOL_ID: 2;
SOURCE 9 SYNTHETIC: YES;
SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 11 ORGANISM_COMMON: HUMAN;
SOURCE 12 ORGANISM_TAXID: 9606;
SOURCE 13 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN HUMANS.
KEYWDS GRB2 SH2 DOMAIN, SIGNALING PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR K.HIGO,M.ODA,N.ITO
REVDAT 3 06-DEC-23 3WA4 1 REMARK
REVDAT 2 08-NOV-23 3WA4 1 REMARK SEQADV LINK
REVDAT 1 26-FEB-14 3WA4 0
JRNL AUTH K.HIGO,T.IKURA,M.ODA,H.MORII,J.TAKAHASHI,R.ABE,N.ITO
JRNL TITL HIGH RESOLUTION CRYSTAL STRUCTURE OF THE GRB2 SH2 DOMAIN
JRNL TITL 2 WITH A PHOSPHOPEPTIDE DERIVED FROM CD28
JRNL REF PLOS ONE V. 8 74482 2013
JRNL REFN ESSN 1932-6203
JRNL PMID 24098653
JRNL DOI 10.1371/JOURNAL.PONE.0074482
REMARK 2
REMARK 2 RESOLUTION. 1.35 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.7.0029
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.54
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8
REMARK 3 NUMBER OF REFLECTIONS : 25113
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) : 0.177
REMARK 3 R VALUE (WORKING SET) : 0.176
REMARK 3 FREE R VALUE : 0.209
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1317
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) : 1.35
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.39
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1820
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.16
REMARK 3 BIN R VALUE (WORKING SET) : 0.1550
REMARK 3 BIN FREE R VALUE SET COUNT : 98
REMARK 3 BIN FREE R VALUE : 0.2450
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 848
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 5
REMARK 3 SOLVENT ATOMS : 64
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.00
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.19000
REMARK 3 B22 (A**2) : 0.19000
REMARK 3 B33 (A**2) : -0.61000
REMARK 3 B12 (A**2) : 0.19000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.058
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.056
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 896 ; 0.020 ; NULL
REMARK 3 BOND LENGTHS OTHERS (A): 842 ; 0.000 ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1208 ; 2.106 ; NULL
REMARK 3 BOND ANGLES OTHERS (DEGREES): 1930 ; 3.681 ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 106 ; 6.815 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 46 ;30.170 ;23.261
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 156 ;12.441 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;20.151 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 122 ; 0.144 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1022 ; 0.014 ;78.290
REMARK 3 GENERAL PLANES OTHERS (A): 235 ; 0.025 ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
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): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): 1738 ;15.236 ; 3.000
REMARK 3 SPHERICITY; FREE ATOMS (A**2): 21 ;24.007 ; 5.000
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 1759 ;11.344 ; 5.000
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 RIDING
REMARK 3 POSITIONS
REMARK 4
REMARK 4 3WA4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-MAY-13.
REMARK 100 THE DEPOSITION ID IS D_1000096077.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 26-OCT-09
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : PHOTON FACTORY
REMARK 200 BEAMLINE : AR-NW12A
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000
REMARK 200 MONOCHROMATOR : SI(111) DOUBLE CRYSTAL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26431
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7
REMARK 200 DATA REDUNDANCY : 20.60
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.05700
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37
REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4
REMARK 200 DATA REDUNDANCY IN SHELL : 21.20
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.49800
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: 3C7I
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 48.13
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES, 1.25M SODIUM ACETATE, 0.1M
REMARK 280 CADMIUM SULFATE, PH 7.5, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z+1/3
REMARK 290 3555 -X+Y,-X,Z+2/3
REMARK 290 4555 -X,-Y,Z+1/2
REMARK 290 5555 Y,-X+Y,Z+5/6
REMARK 290 6555 X-Y,X,Z+1/6
REMARK 290 7555 Y,X,-Z+1/3
REMARK 290 8555 X-Y,-Y,-Z
REMARK 290 9555 -X,-X+Y,-Z+2/3
REMARK 290 10555 -Y,-X,-Z+5/6
REMARK 290 11555 -X+Y,Y,-Z+1/2
REMARK 290 12555 X,X-Y,-Z+1/6
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 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.03000
REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 78.06000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 58.54500
REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 97.57500
REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 19.51500
REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 39.03000
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 78.06000
REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 97.57500
REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 58.54500
REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 19.51500
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2, 3
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
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: MONOMERIC
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
REMARK 350 BIOMOLECULE: 2
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: B
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
REMARK 350 BIOMOLECULE: 3
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 900 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 5790 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
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 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 GLY A 55
REMARK 465 SER A 56
REMARK 465 SER B 189
REMARK 465 PRO B 196
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 ASP B 190 CG OD1 OD2
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES
REMARK 500 ARG A 142 NE - CZ - NH1 ANGL. DEV. = 6.0 DEGREES
REMARK 500 ARG A 142 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES
REMARK 500 MET B 194 CG - SD - CE ANGL. DEV. = 9.7 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 LYS A 64 46.63 -88.74
REMARK 500 TRP A 121 -81.62 -130.83
REMARK 500 TRP A 121 -87.54 -130.83
REMARK 500 VAL A 122 -33.61 -135.67
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY
REMARK 500
REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY
REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER
REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 500 I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI ANGLE
REMARK 500 GLU A 58 -13.04
REMARK 500
REMARK 500 REMARK: NULL
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 CD A 201 CD
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 79 NE2
REMARK 620 2 GLU A 152 OE1 103.4
REMARK 620 3 GLU A 152 OE2 86.4 49.1
REMARK 620 4 ACY A 202 O 91.2 127.5 175.0
REMARK 620 5 ACY A 202 OXT 91.6 79.1 125.6 50.0
REMARK 620 N 1 2 3 4
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 202
DBREF 3WA4 A 60 152 UNP P62993 GRB2_HUMAN 60 152
DBREF 3WA4 B 189 196 UNP P10747 CD28_HUMAN 189 196
SEQADV 3WA4 GLY A 55 UNP P62993 EXPRESSION TAG
SEQADV 3WA4 SER A 56 UNP P62993 EXPRESSION TAG
SEQADV 3WA4 PRO A 57 UNP P62993 EXPRESSION TAG
SEQADV 3WA4 GLU A 58 UNP P62993 EXPRESSION TAG
SEQADV 3WA4 PHE A 59 UNP P62993 EXPRESSION TAG
SEQRES 1 A 98 GLY SER PRO GLU PHE TRP PHE PHE GLY LYS ILE PRO ARG
SEQRES 2 A 98 ALA LYS ALA GLU GLU MET LEU SER LYS GLN ARG HIS ASP
SEQRES 3 A 98 GLY ALA PHE LEU ILE ARG GLU SER GLU SER ALA PRO GLY
SEQRES 4 A 98 ASP PHE SER LEU SER VAL LYS PHE GLY ASN ASP VAL GLN
SEQRES 5 A 98 HIS PHE LYS VAL LEU ARG ASP GLY ALA GLY LYS TYR PHE
SEQRES 6 A 98 LEU TRP VAL VAL LYS PHE ASN SER LEU ASN GLU LEU VAL
SEQRES 7 A 98 ASP TYR HIS ARG SER THR SER VAL SER ARG ASN GLN GLN
SEQRES 8 A 98 ILE PHE LEU ARG ASP ILE GLU
SEQRES 1 B 8 SER ASP PTR MET ASN MET THR PRO
MODRES 3WA4 PTR B 191 TYR O-PHOSPHOTYROSINE
HET PTR B 191 16
HET CD A 201 1
HET ACY A 202 4
HETNAM PTR O-PHOSPHOTYROSINE
HETNAM CD CADMIUM ION
HETNAM ACY ACETIC ACID
HETSYN PTR PHOSPHONOTYROSINE
FORMUL 2 PTR C9 H12 N O6 P
FORMUL 3 CD CD 2+
FORMUL 4 ACY C2 H4 O2
FORMUL 5 HOH *64(H2 O)
HELIX 1 1 PRO A 66 LYS A 76 1 11
HELIX 2 2 SER A 127 HIS A 135 1 9
SHEET 1 A 6 LYS A 124 PHE A 125 0
SHEET 2 A 6 TYR A 118 PHE A 119 -1 N TYR A 118 O PHE A 125
SHEET 3 A 6 ASP A 104 ARG A 112 -1 N LEU A 111 O PHE A 119
SHEET 4 A 6 PHE A 95 PHE A 101 -1 N LEU A 97 O PHE A 108
SHEET 5 A 6 ALA A 82 GLU A 87 -1 N ALA A 82 O LYS A 100
SHEET 6 A 6 ARG A 149 ASP A 150 1 O ARG A 149 N PHE A 83
LINK C ASP B 190 N PTR B 191 1555 1555 1.31
LINK C PTR B 191 N MET B 192 1555 1555 1.32
LINK NE2 HIS A 79 CD CD A 201 1555 1555 2.31
LINK OE1 GLU A 152 CD CD A 201 1555 1555 2.48
LINK OE2 GLU A 152 CD CD A 201 1555 1555 2.59
LINK CD CD A 201 O ACY A 202 1555 1555 2.33
LINK CD CD A 201 OXT ACY A 202 1555 1555 2.36
SITE 1 AC1 4 HIS A 79 ASP A 94 GLU A 152 ACY A 202
SITE 1 AC2 7 ARG A 78 HIS A 79 ASP A 94 ARG A 112
SITE 2 AC2 7 GLU A 152 CD A 201 HOH A 336
CRYST1 59.010 59.010 117.090 90.00 90.00 120.00 P 61 2 2 12
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 0.016946 0.009784 0.000000 0.00000
SCALE2 0.000000 0.019568 0.000000 0.00000
SCALE3 0.000000 0.000000 0.008540 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
