HEADER SIGNALING PROTEIN 21-SEP-16 5LXH TITLE GABARAP-L1 ATG4B LIR COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAMMA-AMINOBUTYRIC ACID RECEPTOR-ASSOCIATED PROTEIN-LIKE 1; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: EARLY ESTROGEN-REGULATED PROTEIN,GABA(A) RECEPTOR-ASSOCIATED COMPND 5 PROTEIN-LIKE 1,GLANDULAR EPITHELIAL CELL PROTEIN 1,GEC-1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: CYSTEINE PROTEASE ATG4B; COMPND 9 CHAIN: E, F, G; COMPND 10 FRAGMENT: UNP RESIDUES 384-393; COMPND 11 SYNONYM: AUT-LIKE 1 CYSTEINE ENDOPEPTIDASE,AUTOPHAGIN-1,AUTOPHAGY- COMPND 12 RELATED CYSTEINE ENDOPEPTIDASE 1,AUTOPHAGY-RELATED PROTEIN 4 HOMOLOG COMPND 13 B,HAPG4B; COMPND 14 EC: 3.4.22.-; COMPND 15 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: GABARAPL1, GEC1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA, PLYSS; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606 KEYWDS LIR, GABARAP, ATG8, LC3, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.MOUILLERON,M.SKYTTE RASMUSSEN,B.KUMAR SHRESTHA,M.WIRTH,K.BOWITZ AUTHOR 2 LARSEN,Y.ABUDU PRINCELY,E.SJOTTEM,S.TOOZE,T.LAMARK,T.JOHANSEN,R.LEE REVDAT 5 17-JAN-24 5LXH 1 REMARK REVDAT 4 31-MAY-17 5LXH 1 JRNL REVDAT 3 22-MAR-17 5LXH 1 JRNL REVDAT 2 15-FEB-17 5LXH 1 JRNL REVDAT 1 08-FEB-17 5LXH 0 JRNL AUTH M.SKYTTE RASMUSSEN,S.MOUILLERON,B.KUMAR SHRESTHA,M.WIRTH, JRNL AUTH 2 R.LEE,K.BOWITZ LARSEN,Y.ABUDU PRINCELY,N.O'REILLY,E.SJTTEM, JRNL AUTH 3 S.A.TOOZE,T.LAMARK,T.JOHANSEN JRNL TITL ATG4B CONTAINS A C-TERMINAL LIR MOTIF IMPORTANT FOR BINDING JRNL TITL 2 AND EFFICIENT CLEAVAGE OF MAMMALIAN ORTHOLOGS OF YEAST ATG8. JRNL REF AUTOPHAGY V. 13 834 2017 JRNL REFN ESSN 1554-8635 JRNL PMID 28287329 JRNL DOI 10.1080/15548627.2017.1287651 REMARK 2 REMARK 2 RESOLUTION. 1.58 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.82 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 55665 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.890 REMARK 3 FREE R VALUE TEST SET COUNT : 2721 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 48.8449 - 4.2152 1.00 3009 152 0.1801 0.1965 REMARK 3 2 4.2152 - 3.3460 1.00 2885 126 0.1536 0.1844 REMARK 3 3 3.3460 - 2.9231 1.00 2864 149 0.1815 0.2138 REMARK 3 4 2.9231 - 2.6558 1.00 2827 136 0.1905 0.2066 REMARK 3 5 2.6558 - 2.4655 1.00 2779 158 0.1959 0.2281 REMARK 3 6 2.4655 - 2.3201 1.00 2809 141 0.1903 0.2337 REMARK 3 7 2.3201 - 2.2039 1.00 2778 155 0.1900 0.2351 REMARK 3 8 2.2039 - 2.1080 1.00 2796 125 0.1891 0.1964 REMARK 3 9 2.1080 - 2.0269 1.00 2787 152 0.1992 0.2347 REMARK 3 10 2.0269 - 1.9569 1.00 2755 151 0.2222 0.2885 REMARK 3 11 1.9569 - 1.8957 0.99 2744 140 0.2428 0.3073 REMARK 3 12 1.8957 - 1.8415 1.00 2769 111 0.2456 0.2840 REMARK 3 13 1.8415 - 1.7930 0.99 2784 144 0.2561 0.2724 REMARK 3 14 1.7930 - 1.7493 0.99 2755 140 0.2801 0.3427 REMARK 3 15 1.7493 - 1.7095 0.99 2730 160 0.3242 0.3493 REMARK 3 16 1.7095 - 1.6731 0.99 2720 144 0.3433 0.3608 REMARK 3 17 1.6731 - 1.6397 0.99 2729 155 0.3673 0.3758 REMARK 3 18 1.6397 - 1.6087 0.98 2704 135 0.3937 0.3951 REMARK 3 19 1.6087 - 1.5800 0.98 2720 147 0.3912 0.4566 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.340 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.017 3344 REMARK 3 ANGLE : 1.428 4552 REMARK 3 CHIRALITY : 0.083 470 REMARK 3 PLANARITY : 0.009 590 REMARK 3 DIHEDRAL : 20.602 2040 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5LXH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-SEP-16. REMARK 100 THE DEPOSITION ID IS D_1200001529. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUL-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.968 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55946 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 REMARK 200 RESOLUTION RANGE LOW (A) : 51.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05000 REMARK 200 FOR THE DATA SET : 10.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.87000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 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: 2R2Q REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.17 M AMSO4, 40 % PEG 4000, 15 % REMARK 280 GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 25.76000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.82150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.94250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.82150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.76000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.94250 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, E 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, F 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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -54.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, G 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 -5 REMARK 465 PRO A -4 REMARK 465 THR A -3 REMARK 465 MET A -2 REMARK 465 GLY A -1 REMARK 465 TYR A 115 REMARK 465 GLY A 116 REMARK 465 LYS A 117 REMARK 465 GLY B -5 REMARK 465 PRO B -4 REMARK 465 THR B -3 REMARK 465 MET B -2 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 GLY B 116 REMARK 465 LYS B 117 REMARK 465 GLY C -5 REMARK 465 PRO C -4 REMARK 465 THR C -3 REMARK 465 MET C -2 REMARK 465 GLY C -1 REMARK 465 SER C 0 REMARK 465 PRO C 37 REMARK 465 LYS C 38 REMARK 465 ALA C 39 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 SER A 0 OG REMARK 470 LYS A 2 CG CD CE NZ REMARK 470 GLN A 4 CG CD OE1 NE2 REMARK 470 GLU A 12 CG CD OE1 OE2 REMARK 470 LYS A 15 CE NZ REMARK 470 LYS A 16 CG CD CE NZ REMARK 470 LYS A 23 CG CD CE NZ REMARK 470 LYS A 38 NZ REMARK 470 ARG A 40 NE CZ NH1 NH2 REMARK 470 LYS A 66 CE NZ REMARK 470 ARG A 71 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 73 CG CD OE1 OE2 REMARK 470 LYS B 2 CG CD CE NZ REMARK 470 GLU B 12 CG CD OE1 OE2 REMARK 470 LYS B 23 CE NZ REMARK 470 LYS B 38 CD CE NZ REMARK 470 ARG B 40 NE CZ NH1 NH2 REMARK 470 LYS B 66 CE NZ REMARK 470 ARG B 71 NE CZ NH1 NH2 REMARK 470 LYS C 16 CG CD CE NZ REMARK 470 LYS C 23 CG CD CE NZ REMARK 470 ARG C 40 CG CD NE CZ NH1 NH2 REMARK 470 LYS C 66 CG CD CE NZ REMARK 470 ASN C 82 CG OD1 ND2 REMARK 470 GLU C 96 OE1 OE2 REMARK 470 LYS C 117 CG CD CE NZ REMARK 470 GLU E 384 CG CD OE1 OE2 REMARK 470 GLU E 386 CG CD OE1 OE2 REMARK 470 LEU E 393 CG CD1 CD2 REMARK 470 LEU F 393 CG CD1 CD2 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 O2 GOL B 205 O HOH B 301 1.96 REMARK 500 OG SER C 113 O1 SO4 C 203 2.04 REMARK 500 O2 GOL B 204 O HOH B 302 2.08 REMARK 500 O HOH B 361 O HOH B 372 2.13 REMARK 500 O HOH B 305 O HOH B 349 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OD2 ASP E 385 O HOH C 303 2454 2.14 REMARK 500 OD1 ASP G 387 O HOH A 302 2355 2.19 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 PRO A 72 CD PRO A 72 N 0.363 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 PRO A 72 N - CD - CG ANGL. DEV. = -16.4 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 ARG A 40 59.63 -94.08 REMARK 500 HIS C 69 70.40 30.03 REMARK 500 HIS C 69 70.70 29.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 375 DISTANCE = 6.69 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 C 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 C 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 204 DBREF 5LXH A 1 117 UNP Q9H0R8 GBRL1_HUMAN 1 117 DBREF 5LXH B 1 117 UNP Q9H0R8 GBRL1_HUMAN 1 117 DBREF 5LXH C 1 117 UNP Q9H0R8 GBRL1_HUMAN 1 117 DBREF 5LXH E 384 393 UNP Q9Y4P1 ATG4B_HUMAN 384 393 DBREF 5LXH F 384 393 UNP Q9Y4P1 ATG4B_HUMAN 384 393 DBREF 5LXH G 384 393 UNP Q9Y4P1 ATG4B_HUMAN 384 393 SEQADV 5LXH GLY A -5 UNP Q9H0R8 EXPRESSION TAG SEQADV 5LXH PRO A -4 UNP Q9H0R8 EXPRESSION TAG SEQADV 5LXH THR A -3 UNP Q9H0R8 EXPRESSION TAG SEQADV 5LXH MET A -2 UNP Q9H0R8 EXPRESSION TAG SEQADV 5LXH GLY A -1 UNP Q9H0R8 EXPRESSION TAG SEQADV 5LXH SER A 0 UNP Q9H0R8 EXPRESSION TAG SEQADV 5LXH GLY B -5 UNP Q9H0R8 EXPRESSION TAG SEQADV 5LXH PRO B -4 UNP Q9H0R8 EXPRESSION TAG SEQADV 5LXH THR B -3 UNP Q9H0R8 EXPRESSION TAG SEQADV 5LXH MET B -2 UNP Q9H0R8 EXPRESSION TAG SEQADV 5LXH GLY B -1 UNP Q9H0R8 EXPRESSION TAG SEQADV 5LXH SER B 0 UNP Q9H0R8 EXPRESSION TAG SEQADV 5LXH GLY C -5 UNP Q9H0R8 EXPRESSION TAG SEQADV 5LXH PRO C -4 UNP Q9H0R8 EXPRESSION TAG SEQADV 5LXH THR C -3 UNP Q9H0R8 EXPRESSION TAG SEQADV 5LXH MET C -2 UNP Q9H0R8 EXPRESSION TAG SEQADV 5LXH GLY C -1 UNP Q9H0R8 EXPRESSION TAG SEQADV 5LXH SER C 0 UNP Q9H0R8 EXPRESSION TAG SEQRES 1 A 123 GLY PRO THR MET GLY SER MET LYS PHE GLN TYR LYS GLU SEQRES 2 A 123 ASP HIS PRO PHE GLU TYR ARG LYS LYS GLU GLY GLU LYS SEQRES 3 A 123 ILE ARG LYS LYS TYR PRO ASP ARG VAL PRO VAL ILE VAL SEQRES 4 A 123 GLU LYS ALA PRO LYS ALA ARG VAL PRO ASP LEU ASP LYS SEQRES 5 A 123 ARG LYS TYR LEU VAL PRO SER ASP LEU THR VAL GLY GLN SEQRES 6 A 123 PHE TYR PHE LEU ILE ARG LYS ARG ILE HIS LEU ARG PRO SEQRES 7 A 123 GLU ASP ALA LEU PHE PHE PHE VAL ASN ASN THR ILE PRO SEQRES 8 A 123 PRO THR SER ALA THR MET GLY GLN LEU TYR GLU ASP ASN SEQRES 9 A 123 HIS GLU GLU ASP TYR PHE LEU TYR VAL ALA TYR SER ASP SEQRES 10 A 123 GLU SER VAL TYR GLY LYS SEQRES 1 B 123 GLY PRO THR MET GLY SER MET LYS PHE GLN TYR LYS GLU SEQRES 2 B 123 ASP HIS PRO PHE GLU TYR ARG LYS LYS GLU GLY GLU LYS SEQRES 3 B 123 ILE ARG LYS LYS TYR PRO ASP ARG VAL PRO VAL ILE VAL SEQRES 4 B 123 GLU LYS ALA PRO LYS ALA ARG VAL PRO ASP LEU ASP LYS SEQRES 5 B 123 ARG LYS TYR LEU VAL PRO SER ASP LEU THR VAL GLY GLN SEQRES 6 B 123 PHE TYR PHE LEU ILE ARG LYS ARG ILE HIS LEU ARG PRO SEQRES 7 B 123 GLU ASP ALA LEU PHE PHE PHE VAL ASN ASN THR ILE PRO SEQRES 8 B 123 PRO THR SER ALA THR MET GLY GLN LEU TYR GLU ASP ASN SEQRES 9 B 123 HIS GLU GLU ASP TYR PHE LEU TYR VAL ALA TYR SER ASP SEQRES 10 B 123 GLU SER VAL TYR GLY LYS SEQRES 1 C 123 GLY PRO THR MET GLY SER MET LYS PHE GLN TYR LYS GLU SEQRES 2 C 123 ASP HIS PRO PHE GLU TYR ARG LYS LYS GLU GLY GLU LYS SEQRES 3 C 123 ILE ARG LYS LYS TYR PRO ASP ARG VAL PRO VAL ILE VAL SEQRES 4 C 123 GLU LYS ALA PRO LYS ALA ARG VAL PRO ASP LEU ASP LYS SEQRES 5 C 123 ARG LYS TYR LEU VAL PRO SER ASP LEU THR VAL GLY GLN SEQRES 6 C 123 PHE TYR PHE LEU ILE ARG LYS ARG ILE HIS LEU ARG PRO SEQRES 7 C 123 GLU ASP ALA LEU PHE PHE PHE VAL ASN ASN THR ILE PRO SEQRES 8 C 123 PRO THR SER ALA THR MET GLY GLN LEU TYR GLU ASP ASN SEQRES 9 C 123 HIS GLU GLU ASP TYR PHE LEU TYR VAL ALA TYR SER ASP SEQRES 10 C 123 GLU SER VAL TYR GLY LYS SEQRES 1 E 10 GLU ASP GLU ASP PHE GLU ILE LEU SER LEU SEQRES 1 F 10 GLU ASP GLU ASP PHE GLU ILE LEU SER LEU SEQRES 1 G 10 GLU ASP GLU ASP PHE GLU ILE LEU SER LEU HET SO4 A 201 5 HET SO4 B 201 5 HET SO4 B 202 5 HET SO4 B 203 5 HET GOL B 204 6 HET GOL B 205 6 HET SO4 C 201 5 HET SO4 C 202 5 HET SO4 C 203 5 HET GOL C 204 6 HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 7 SO4 7(O4 S 2-) FORMUL 11 GOL 3(C3 H8 O3) FORMUL 17 HOH *218(H2 O) HELIX 1 AA1 PHE A 3 ASP A 8 1 6 HELIX 2 AA2 PRO A 10 TYR A 25 1 16 HELIX 3 AA3 THR A 56 HIS A 69 1 14 HELIX 4 AA4 THR A 90 HIS A 99 1 10 HELIX 5 AA5 PHE B 3 HIS B 9 1 7 HELIX 6 AA6 PRO B 10 TYR B 25 1 16 HELIX 7 AA7 THR B 56 HIS B 69 1 14 HELIX 8 AA8 THR B 90 HIS B 99 1 10 HELIX 9 AA9 PHE C 3 ASP C 8 1 6 HELIX 10 AB1 PRO C 10 TYR C 25 1 16 HELIX 11 AB2 THR C 56 HIS C 69 1 14 HELIX 12 AB3 THR C 90 HIS C 99 1 10 HELIX 13 AB4 GLU E 384 PHE E 388 5 5 SHEET 1 AA1 5 PHE A 77 PHE A 79 0 SHEET 2 AA1 5 LEU A 105 SER A 110 -1 O ALA A 108 N PHE A 79 SHEET 3 AA1 5 ARG A 28 LYS A 35 1 N ILE A 32 O LEU A 105 SHEET 4 AA1 5 LYS A 48 PRO A 52 -1 O VAL A 51 N VAL A 29 SHEET 5 AA1 5 GLU E 389 ILE E 390 1 O GLU E 389 N LEU A 50 SHEET 1 AA2 5 ASP B 74 PHE B 79 0 SHEET 2 AA2 5 LEU B 105 SER B 113 -1 O ALA B 108 N PHE B 79 SHEET 3 AA2 5 ARG B 28 LYS B 35 1 N ILE B 32 O LEU B 105 SHEET 4 AA2 5 LYS B 48 PRO B 52 -1 O TYR B 49 N VAL B 31 SHEET 5 AA2 5 GLU F 389 ILE F 390 1 O GLU F 389 N LEU B 50 SHEET 1 AA3 5 ASP C 74 PHE C 79 0 SHEET 2 AA3 5 LEU C 105 SER C 113 -1 O ALA C 108 N PHE C 79 SHEET 3 AA3 5 ARG C 28 LYS C 35 1 N ILE C 32 O LEU C 105 SHEET 4 AA3 5 LYS C 48 PRO C 52 -1 O TYR C 49 N VAL C 31 SHEET 5 AA3 5 GLU G 389 ILE G 390 1 O GLU G 389 N LYS C 48 SITE 1 AC1 8 ASP A 45 LYS A 46 ARG A 47 LYS A 48 SITE 2 AC1 8 HOH A 303 HOH A 341 HIS B 69 ASP E 387 SITE 1 AC2 8 HIS A 69 ASP B 45 LYS B 46 ARG B 47 SITE 2 AC2 8 LYS B 48 SO4 B 203 HOH B 333 ASP F 387 SITE 1 AC3 2 ARG B 14 GLU C 101 SITE 1 AC4 8 TYR B 5 ASP B 8 HIS B 9 LYS B 48 SITE 2 AC4 8 SO4 B 201 HOH B 311 HOH B 319 THR C 83 SITE 1 AC5 9 PHE B 79 VAL B 80 ASN B 81 ASN B 82 SITE 2 AC5 9 TYR B 106 ALA B 108 HOH B 302 HOH B 315 SITE 3 AC5 9 HOH B 363 SITE 1 AC6 6 HOH A 315 ARG B 22 GLU B 96 TYR B 103 SITE 2 AC6 6 HOH B 301 HOH B 334 SITE 1 AC7 8 GLN A 93 GLU A 96 LYS C 46 ARG C 47 SITE 2 AC7 8 LYS C 48 SO4 C 202 HOH C 302 ASP G 387 SITE 1 AC8 6 TYR C 5 ASP C 8 HIS C 9 LYS C 48 SITE 2 AC8 6 SO4 C 201 HOH C 302 SITE 1 AC9 8 ARG C 71 GLU C 73 ASP C 74 SER C 113 SITE 2 AC9 8 VAL C 114 TYR C 115 GLY C 116 LYS C 117 SITE 1 AD1 5 GLU C 34 LYS C 35 ARG C 47 HOH C 310 SITE 2 AD1 5 HOH C 334 CRYST1 51.520 79.885 97.643 90.00 90.00 90.00 P 21 21 21 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 0.019410 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012518 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010241 0.00000