HEADER STRUCTURAL PROTEIN 22-FEB-15 4YDP TITLE CRYSTAL STRUCTURE OF N-TERMINAL PDZ DOMAIN OF ZASP IN COMPLEX WITH TITLE 2 MYOTILIN C-TERMINAL PEPTIDE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIM DOMAIN-BINDING PROTEIN 3; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PROTEIN CYPHER,Z-BAND ALTERNATIVELY SPLICED PDZ-MOTIF COMPND 5 PROTEIN; COMPND 6 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: LDB3, KIAA0613, ZASP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ZASP/LDB3, MYOTILIN, STRIATED MUSCLE Z-DISC, SARCOMERE, STRUCTURAL KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR I.GRISHKOVSKAYA,A.ONIPE,G.KONTAXIS,K.DJINOVIC-CARUGO REVDAT 2 10-JAN-24 4YDP 1 REMARK REVDAT 1 29-JUN-16 4YDP 0 JRNL AUTH I.GRISHKOVSKAYA,A.ONIPE,G.KONTAXIS,K.DJINOVIC-CARUGO JRNL TITL CRYSTAL STRUCTURE OF N-TERMINAL PDZ DOMAIN OF ZASP IN JRNL TITL 2 COMPLEX WITH MYOTILIN C-TERMINAL PEPTIDE. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.75 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.4 REMARK 3 NUMBER OF REFLECTIONS : 23381 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) : 0.125 REMARK 3 R VALUE (WORKING SET) : 0.124 REMARK 3 FREE R VALUE : 0.157 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1195 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) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1053 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 54.34 REMARK 3 BIN R VALUE (WORKING SET) : 0.1800 REMARK 3 BIN FREE R VALUE SET COUNT : 48 REMARK 3 BIN FREE R VALUE : 0.2280 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1240 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 54 REMARK 3 SOLVENT ATOMS : 145 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.82000 REMARK 3 B22 (A**2) : 2.02000 REMARK 3 B33 (A**2) : 1.80000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.57000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.014 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.012 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.031 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.656 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.978 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.971 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1309 ; 0.010 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 1257 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1783 ; 1.475 ; 1.950 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2873 ; 0.961 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 177 ; 6.289 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 46 ;36.536 ;26.087 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 211 ;10.465 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 2 ; 3.384 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 211 ; 0.087 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1489 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 281 ; 0.003 ; 0.020 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): 692 ; 1.175 ; 1.196 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 691 ; 1.174 ; 1.194 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 860 ; 1.509 ; 1.797 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): 2566 ; 2.327 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 56 ;27.277 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 2637 ; 8.653 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 1 83 B 1 83 4473 0.100 0.050 REMARK 3 REMARK 3 TWIN DETAILS REMARK 3 NUMBER OF TWIN DOMAINS : 2 REMARK 3 TWIN DOMAIN : 1 REMARK 3 TWIN OPERATOR : H, K, L REMARK 3 TWIN FRACTION : 0.666 REMARK 3 TWIN DOMAIN : 2 REMARK 3 TWIN OPERATOR : H+L, -K, -L REMARK 3 TWIN FRACTION : 0.334 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 : 1.00 REMARK 3 ION PROBE RADIUS : 0.70 REMARK 3 SHRINKAGE RADIUS : 0.70 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4YDP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1000207273. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24577 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 47.750 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.4 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 61.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.30100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 2PKT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 6000, IMIDAZOLE, PH 8.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 295.15K 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 47.75000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 ALA A 0 REMARK 465 LYS A 84 REMARK 465 ALA B 0 REMARK 465 LYS B 84 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 16 CD NE CZ NH1 NH2 REMARK 480 LYS A 21 CE REMARK 480 GLN A 45 CG CD REMARK 480 LYS A 70 CD CE NZ REMARK 480 LYS A 82 CD CE REMARK 480 ARG B 16 CD NE CZ NH1 NH2 REMARK 480 LYS B 37 CE REMARK 480 GLN B 66 CD REMARK 480 LYS B 82 CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 C GLU A 102 N LEU A 103 1.33 REMARK 500 C GLU B 102 N LEU B 103 1.33 REMARK 500 C GLU B 101 N GLU B 102 1.33 REMARK 500 C GLU A 101 N GLU A 102 1.34 REMARK 500 O HOH B 211 O HOH B 220 1.63 REMARK 500 O HOH B 261 O HOH B 266 1.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG A 16 CZ ARG A 16 NH1 0.214 REMARK 500 ARG A 16 CZ ARG A 16 NH2 0.255 REMARK 500 GLN A 45 CB GLN A 45 CG -0.174 REMARK 500 LYS A 82 CG LYS A 82 CD 0.267 REMARK 500 LYS B 37 CE LYS B 37 NZ 0.151 REMARK 500 GLN B 66 CD GLN B 66 NE2 -0.279 REMARK 500 LYS B 82 CD LYS B 82 CE -0.231 REMARK 500 REMARK 500 REMARK: NULL 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 16 NH1 - CZ - NH2 ANGL. DEV. = 7.9 DEGREES REMARK 500 ARG A 16 NE - CZ - NH1 ANGL. DEV. = -13.1 DEGREES REMARK 500 ARG B 16 NE - CZ - NH1 ANGL. DEV. = 3.0 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 TYR A 74 -67.40 -168.62 REMARK 500 TYR B 74 -65.97 -169.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 16 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 GLU A 101 REMARK 610 GLU A 102 REMARK 610 GLU B 101 REMARK 610 GLU B 102 REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 GLU A 101 REMARK 615 GLU A 102 REMARK 615 GLU B 101 REMARK 615 GLU B 102 REMARK 615 LEU B 103 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GLU A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GLU A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LEU A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GLU B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GLU B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LEU B 103 DBREF 4YDP A 1 84 UNP O75112 LDB3_HUMAN 1 84 DBREF 4YDP B 1 84 UNP O75112 LDB3_HUMAN 1 84 SEQADV 4YDP ALA A 0 UNP O75112 EXPRESSION TAG SEQADV 4YDP ALA A 2 UNP O75112 SER 2 ENGINEERED MUTATION SEQADV 4YDP ALA B 0 UNP O75112 EXPRESSION TAG SEQADV 4YDP ALA B 2 UNP O75112 SER 2 ENGINEERED MUTATION SEQRES 1 A 85 ALA MET ALA TYR SER VAL THR LEU THR GLY PRO GLY PRO SEQRES 2 A 85 TRP GLY PHE ARG LEU GLN GLY GLY LYS ASP PHE ASN MET SEQRES 3 A 85 PRO LEU THR ILE SER ARG ILE THR PRO GLY SER LYS ALA SEQRES 4 A 85 ALA GLN SER GLN LEU SER GLN GLY ASP LEU VAL VAL ALA SEQRES 5 A 85 ILE ASP GLY VAL ASN THR ASP THR MET THR HIS LEU GLU SEQRES 6 A 85 ALA GLN ASN LYS ILE LYS SER ALA SER TYR ASN LEU SER SEQRES 7 A 85 LEU THR LEU GLN LYS SER LYS SEQRES 1 B 85 ALA MET ALA TYR SER VAL THR LEU THR GLY PRO GLY PRO SEQRES 2 B 85 TRP GLY PHE ARG LEU GLN GLY GLY LYS ASP PHE ASN MET SEQRES 3 B 85 PRO LEU THR ILE SER ARG ILE THR PRO GLY SER LYS ALA SEQRES 4 B 85 ALA GLN SER GLN LEU SER GLN GLY ASP LEU VAL VAL ALA SEQRES 5 B 85 ILE ASP GLY VAL ASN THR ASP THR MET THR HIS LEU GLU SEQRES 6 B 85 ALA GLN ASN LYS ILE LYS SER ALA SER TYR ASN LEU SER SEQRES 7 B 85 LEU THR LEU GLN LYS SER LYS HET GLU A 101 9 HET GLU A 102 9 HET LEU A 103 9 HET GLU B 101 9 HET GLU B 102 9 HET LEU B 103 9 HETNAM GLU GLUTAMIC ACID HETNAM LEU LEUCINE FORMUL 3 GLU 4(C5 H9 N O4) FORMUL 5 LEU 2(C6 H13 N O2) FORMUL 9 HOH *145(H2 O) HELIX 1 AA1 LYS A 21 ASN A 24 5 4 HELIX 2 AA2 SER A 36 SER A 41 1 6 HELIX 3 AA3 THR A 61 SER A 71 1 11 HELIX 4 AA4 LYS B 21 ASN B 24 5 4 HELIX 5 AA5 SER B 36 SER B 41 1 6 HELIX 6 AA6 THR B 61 SER B 71 1 11 SHEET 1 AA1 4 ALA A 2 LEU A 7 0 SHEET 2 AA1 4 LEU A 76 GLN A 81 -1 O LEU A 80 N TYR A 3 SHEET 3 AA1 4 LEU A 48 ILE A 52 -1 N ALA A 51 O THR A 79 SHEET 4 AA1 4 VAL A 55 ASN A 56 -1 O VAL A 55 N ILE A 52 SHEET 1 AA2 2 PHE A 15 GLY A 20 0 SHEET 2 AA2 2 MET A 25 ILE A 32 -1 O SER A 30 N ARG A 16 SHEET 1 AA3 4 ALA B 2 LEU B 7 0 SHEET 2 AA3 4 LEU B 76 GLN B 81 -1 O LEU B 80 N TYR B 3 SHEET 3 AA3 4 LEU B 48 ILE B 52 -1 N ALA B 51 O THR B 79 SHEET 4 AA3 4 VAL B 55 ASN B 56 -1 O VAL B 55 N ILE B 52 SHEET 1 AA4 2 PHE B 15 GLY B 20 0 SHEET 2 AA4 2 MET B 25 ILE B 32 -1 O SER B 30 N ARG B 16 CISPEP 1 GLY A 9 PRO A 10 0 -0.32 CISPEP 2 GLY A 11 PRO A 12 0 7.43 CISPEP 3 GLY B 9 PRO B 10 0 0.86 CISPEP 4 GLY B 11 PRO B 12 0 6.85 SITE 1 AC1 6 GLN A 66 GLU A 102 LEU A 103 HOH A 223 SITE 2 AC1 6 HOH A 228 HOH A 255 SITE 1 AC2 9 GLY A 14 ARG A 16 THR A 33 ASP A 58 SITE 2 AC2 9 THR A 59 GLU A 101 LEU A 103 HOH A 208 SITE 3 AC2 9 HOH A 216 SITE 1 AC3 8 PRO A 12 TRP A 13 GLY A 14 PHE A 15 SITE 2 AC3 8 GLN A 66 GLU A 101 GLU A 102 HOH A 259 SITE 1 AC4 3 GLU B 102 LEU B 103 HOH B 256 SITE 1 AC5 3 GLU B 101 LEU B 103 HOH B 204 SITE 1 AC6 8 PRO B 12 TRP B 13 GLY B 14 PHE B 15 SITE 2 AC6 8 LEU B 17 GLU B 101 GLU B 102 HOH B 269 CRYST1 28.900 95.500 28.900 90.00 120.00 90.00 P 1 21 1 4 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 0.034602 0.000000 0.019978 0.00000 SCALE2 0.000000 0.010471 0.000000 0.00000 SCALE3 0.000000 0.000000 0.039955 0.00000