HEADER PROTEIN FIBRIL 27-OCT-20 7AS7 TITLE CRYSTAL STRUCTURE OF THE GCD-ASSOCIATED TGFBIP MUTANT R124H COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSFORMING GROWTH FACTOR-BETA-INDUCED PROTEIN IG-H3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BETA IG-H3,KERATO-EPITHELIN,RGD-CONTAINING COLLAGEN- COMPND 5 ASSOCIATED PROTEIN,RGD-CAP; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TGFBI, BIGH3; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293 KEYWDS GRANULAR CORNEAL DYSTROPHY, LATTICE CORNEAL DYSTROPHY, PROTEIN KEYWDS 2 AGGREGATION, EXTRACELLULAR MATRIX PROTEIN, PROTEIN FIBRIL EXPDTA X-RAY DIFFRACTION AUTHOR G.R.ANDERSEN,T.A.F.GADEBERG,N.S.NIELSEN,J.J.ENGHILD REVDAT 3 31-JAN-24 7AS7 1 REMARK REVDAT 2 07-JUL-21 7AS7 1 JRNL REVDAT 1 23-DEC-20 7AS7 0 JRNL AUTH N.S.NIELSEN,T.A.F.GADEBERG,E.T.POULSEN,S.L.HARWOOD, JRNL AUTH 2 C.E.WEBERSKOV,J.S.PEDERSEN,G.R.ANDERSEN,J.J.ENGHILD JRNL TITL MUTATION-INDUCED DIMERIZATION OF TRANSFORMING GROWTH JRNL TITL 2 FACTOR-BETA-INDUCED PROTEIN MAY DRIVE PROTEIN AGGREGATION IN JRNL TITL 3 GRANULAR CORNEAL DYSTROPHY. JRNL REF J.BIOL.CHEM. V. 297 00858 2021 JRNL REFN ESSN 1083-351X JRNL PMID 34097874 JRNL DOI 10.1016/J.JBC.2021.100858 REMARK 2 REMARK 2 RESOLUTION. 2.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 23008 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.285 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.680 REMARK 3 FREE R VALUE TEST SET COUNT : 1998 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 45.8500 - 6.3800 1.00 1613 154 0.1636 0.2053 REMARK 3 2 6.3800 - 5.0700 1.00 1522 144 0.1898 0.2893 REMARK 3 3 5.0700 - 4.4300 1.00 1523 145 0.1578 0.2205 REMARK 3 4 4.4300 - 4.0200 1.00 1510 144 0.1664 0.2187 REMARK 3 5 4.0200 - 3.7300 1.00 1510 144 0.2066 0.2872 REMARK 3 6 3.7300 - 3.5100 1.00 1489 140 0.2290 0.3185 REMARK 3 7 3.5100 - 3.3400 1.00 1496 142 0.2541 0.3803 REMARK 3 8 3.3400 - 3.1900 1.00 1486 141 0.2769 0.3667 REMARK 3 9 3.1900 - 3.0700 1.00 1491 143 0.2678 0.3696 REMARK 3 10 3.0700 - 2.9600 1.00 1486 142 0.3103 0.3887 REMARK 3 11 2.9600 - 2.8700 1.00 1474 139 0.3152 0.3892 REMARK 3 12 2.8700 - 2.7900 1.00 1476 141 0.3180 0.3310 REMARK 3 13 2.7900 - 2.7200 0.99 1496 143 0.3437 0.4454 REMARK 3 14 2.7200 - 2.6500 1.00 1438 136 0.3805 0.3986 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.30 REMARK 3 SHRINKAGE RADIUS : 1.00 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.533 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.009 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 66.86 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 78.37 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 : 0.013 4539 REMARK 3 ANGLE : 1.550 6162 REMARK 3 CHIRALITY : 0.075 739 REMARK 3 PLANARITY : 0.011 795 REMARK 3 DIHEDRAL : 8.989 2759 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 47 THROUGH 94 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.1715 77.4633 31.8106 REMARK 3 T TENSOR REMARK 3 T11: 1.5794 T22: 1.4301 REMARK 3 T33: 1.5249 T12: -0.2051 REMARK 3 T13: -0.5600 T23: 0.3059 REMARK 3 L TENSOR REMARK 3 L11: 4.8801 L22: 0.4936 REMARK 3 L33: 5.1199 L12: 0.7222 REMARK 3 L13: 4.9891 L23: 0.7801 REMARK 3 S TENSOR REMARK 3 S11: -0.2854 S12: 0.7636 S13: 1.2900 REMARK 3 S21: 0.9451 S22: -0.6660 S23: -0.2687 REMARK 3 S31: -0.7408 S32: 0.3891 S33: 0.6250 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 95 THROUGH 189 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.5211 56.9965 21.3627 REMARK 3 T TENSOR REMARK 3 T11: 0.5674 T22: 0.6978 REMARK 3 T33: 0.6024 T12: -0.0620 REMARK 3 T13: -0.0459 T23: 0.0808 REMARK 3 L TENSOR REMARK 3 L11: 6.0712 L22: 4.1929 REMARK 3 L33: 3.5452 L12: -1.6693 REMARK 3 L13: 0.2147 L23: 0.4637 REMARK 3 S TENSOR REMARK 3 S11: 0.0148 S12: 0.2852 S13: 0.2697 REMARK 3 S21: 0.0223 S22: -0.2743 S23: -0.1377 REMARK 3 S31: 0.0693 S32: 0.0591 S33: 0.2382 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 190 THROUGH 367 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.2155 52.0286 45.2945 REMARK 3 T TENSOR REMARK 3 T11: 0.4997 T22: 0.5841 REMARK 3 T33: 0.5779 T12: -0.0303 REMARK 3 T13: -0.0070 T23: 0.0163 REMARK 3 L TENSOR REMARK 3 L11: 3.4605 L22: 0.4635 REMARK 3 L33: 7.9383 L12: -1.1457 REMARK 3 L13: 4.6397 L23: -1.3532 REMARK 3 S TENSOR REMARK 3 S11: -0.1857 S12: 0.0506 S13: 0.1952 REMARK 3 S21: 0.0681 S22: 0.0548 S23: -0.0079 REMARK 3 S31: -0.1626 S32: 0.3087 S33: 0.1404 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 368 THROUGH 524 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.7740 61.7731 83.7247 REMARK 3 T TENSOR REMARK 3 T11: 0.5760 T22: 1.0448 REMARK 3 T33: 0.6956 T12: 0.0058 REMARK 3 T13: -0.0533 T23: -0.0454 REMARK 3 L TENSOR REMARK 3 L11: 0.1693 L22: 1.9917 REMARK 3 L33: 3.6492 L12: -0.3240 REMARK 3 L13: -0.6443 L23: 2.2345 REMARK 3 S TENSOR REMARK 3 S11: -0.0472 S12: -0.1502 S13: 0.1243 REMARK 3 S21: 0.0114 S22: 0.2964 S23: -0.2311 REMARK 3 S31: 0.0825 S32: 0.7102 S33: -0.3010 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 525 THROUGH 572 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.4088 79.6130 111.0116 REMARK 3 T TENSOR REMARK 3 T11: 0.6302 T22: 0.9807 REMARK 3 T33: 0.6755 T12: 0.0433 REMARK 3 T13: 0.0592 T23: -0.0424 REMARK 3 L TENSOR REMARK 3 L11: 1.8801 L22: 7.0590 REMARK 3 L33: 7.9974 L12: 0.7051 REMARK 3 L13: 1.4749 L23: 6.1862 REMARK 3 S TENSOR REMARK 3 S11: -0.3372 S12: -0.3559 S13: 0.1424 REMARK 3 S21: 0.9037 S22: 0.1363 S23: 0.3852 REMARK 3 S31: 0.5847 S32: -0.0320 S33: 0.3234 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 573 THROUGH 637 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.9359 78.4625 96.9016 REMARK 3 T TENSOR REMARK 3 T11: 0.6009 T22: 0.7934 REMARK 3 T33: 0.6644 T12: -0.0346 REMARK 3 T13: 0.0323 T23: -0.0180 REMARK 3 L TENSOR REMARK 3 L11: 4.8469 L22: 2.4699 REMARK 3 L33: 7.0974 L12: 0.0914 REMARK 3 L13: 2.9134 L23: 0.5944 REMARK 3 S TENSOR REMARK 3 S11: -0.0424 S12: 0.3456 S13: -0.1110 REMARK 3 S21: -0.2444 S22: 0.2653 S23: 0.5592 REMARK 3 S31: -0.2937 S32: 0.2199 S33: -0.1695 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 7AS7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1292112004. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUN-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P14 (MX2) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23038 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.650 REMARK 200 RESOLUTION RANGE LOW (A) : 45.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.20600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.7100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: 5NV6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M DL-MALIC ACID PH 7.0, 12% W/V REMARK 280 PEG 3350, VAPOR DIFFUSION, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 107.01000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 107.01000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 38.68500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 46.93500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 38.68500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 46.93500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 107.01000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 38.68500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 46.93500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 107.01000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 38.68500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 46.93500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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 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 45 REMARK 465 PRO A 46 REMARK 465 LYS A 66 REMARK 465 GLN A 67 REMARK 465 TRP A 68 REMARK 465 TYR A 69 REMARK 465 HIS A 635 REMARK 465 HIS A 636 REMARK 465 HIS A 637 REMARK 465 HIS A 638 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 N GLN A 70 O HOH A 701 2.06 REMARK 500 O HOH A 742 O HOH A 745 2.16 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 OE2 GLU A 286 OG SER A 290 3655 2.13 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 LEU A 265 CB - CG - CD1 ANGL. DEV. = -10.3 DEGREES REMARK 500 CYS A 317 CA - CB - SG ANGL. DEV. = 9.2 DEGREES REMARK 500 LEU A 382 CA - CB - CG ANGL. DEV. = 14.5 DEGREES REMARK 500 LEU A 382 CB - CG - CD2 ANGL. DEV. = -10.4 DEGREES REMARK 500 TYR A 450 CA - CB - CG ANGL. DEV. = 13.2 DEGREES REMARK 500 TYR A 450 CB - CG - CD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 TYR A 450 CB - CG - CD1 ANGL. DEV. = 4.9 DEGREES REMARK 500 LEU A 498 CA - CB - CG ANGL. DEV. = 18.1 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 THR A 57 -156.03 -139.45 REMARK 500 ASN A 58 -11.38 -142.92 REMARK 500 THR A 63 -155.78 -118.07 REMARK 500 ASN A 64 -124.76 -85.39 REMARK 500 ARG A 71 -76.02 -86.85 REMARK 500 VAL A 91 -155.07 65.15 REMARK 500 GLU A 94 -107.53 54.05 REMARK 500 CYS A 97 81.44 48.75 REMARK 500 SER A 115 56.84 -104.73 REMARK 500 GLU A 126 8.99 58.12 REMARK 500 LYS A 127 -26.56 -141.81 REMARK 500 ILE A 165 -76.31 -115.22 REMARK 500 ASN A 213 44.33 33.35 REMARK 500 LEU A 371 77.40 -101.15 REMARK 500 SER A 375 0.84 -67.60 REMARK 500 GLU A 385 61.97 -110.29 REMARK 500 ASP A 442 152.16 62.46 REMARK 500 GLU A 475 -129.34 55.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 CYS A 84 CYS A 85 -145.86 REMARK 500 CYS A 317 ALA A 318 -141.45 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 TYR A 450 0.05 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5NV6 RELATED DB: PDB REMARK 900 WILDTYPE STRUCTURE DBREF 7AS7 A 45 632 UNP Q15582 BGH3_HUMAN 45 632 SEQADV 7AS7 HIS A 124 UNP Q15582 ARG 124 ENGINEERED MUTATION SEQADV 7AS7 HIS A 633 UNP Q15582 EXPRESSION TAG SEQADV 7AS7 HIS A 634 UNP Q15582 EXPRESSION TAG SEQADV 7AS7 HIS A 635 UNP Q15582 EXPRESSION TAG SEQADV 7AS7 HIS A 636 UNP Q15582 EXPRESSION TAG SEQADV 7AS7 HIS A 637 UNP Q15582 EXPRESSION TAG SEQADV 7AS7 HIS A 638 UNP Q15582 EXPRESSION TAG SEQRES 1 A 594 GLY PRO ASN VAL CYS ALA VAL GLN LYS VAL ILE GLY THR SEQRES 2 A 594 ASN ARG LYS TYR PHE THR ASN CYS LYS GLN TRP TYR GLN SEQRES 3 A 594 ARG LYS ILE CYS GLY LYS SER THR VAL ILE SER TYR GLU SEQRES 4 A 594 CYS CYS PRO GLY TYR GLU LYS VAL PRO GLY GLU LYS GLY SEQRES 5 A 594 CYS PRO ALA ALA LEU PRO LEU SER ASN LEU TYR GLU THR SEQRES 6 A 594 LEU GLY VAL VAL GLY SER THR THR THR GLN LEU TYR THR SEQRES 7 A 594 ASP HIS THR GLU LYS LEU ARG PRO GLU MET GLU GLY PRO SEQRES 8 A 594 GLY SER PHE THR ILE PHE ALA PRO SER ASN GLU ALA TRP SEQRES 9 A 594 ALA SER LEU PRO ALA GLU VAL LEU ASP SER LEU VAL SER SEQRES 10 A 594 ASN VAL ASN ILE GLU LEU LEU ASN ALA LEU ARG TYR HIS SEQRES 11 A 594 MET VAL GLY ARG ARG VAL LEU THR ASP GLU LEU LYS HIS SEQRES 12 A 594 GLY MET THR LEU THR SER MET TYR GLN ASN SER ASN ILE SEQRES 13 A 594 GLN ILE HIS HIS TYR PRO ASN GLY ILE VAL THR VAL ASN SEQRES 14 A 594 CYS ALA ARG LEU LEU LYS ALA ASP HIS HIS ALA THR ASN SEQRES 15 A 594 GLY VAL VAL HIS LEU ILE ASP LYS VAL ILE SER THR ILE SEQRES 16 A 594 THR ASN ASN ILE GLN GLN ILE ILE GLU ILE GLU ASP THR SEQRES 17 A 594 PHE GLU THR LEU ARG ALA ALA VAL ALA ALA SER GLY LEU SEQRES 18 A 594 ASN THR MET LEU GLU GLY ASN GLY GLN TYR THR LEU LEU SEQRES 19 A 594 ALA PRO THR ASN GLU ALA PHE GLU LYS ILE PRO SER GLU SEQRES 20 A 594 THR LEU ASN ARG ILE LEU GLY ASP PRO GLU ALA LEU ARG SEQRES 21 A 594 ASP LEU LEU ASN ASN HIS ILE LEU LYS SER ALA MET CYS SEQRES 22 A 594 ALA GLU ALA ILE VAL ALA GLY LEU SER VAL GLU THR LEU SEQRES 23 A 594 GLU GLY THR THR LEU GLU VAL GLY CYS SER GLY ASP MET SEQRES 24 A 594 LEU THR ILE ASN GLY LYS ALA ILE ILE SER ASN LYS ASP SEQRES 25 A 594 ILE LEU ALA THR ASN GLY VAL ILE HIS TYR ILE ASP GLU SEQRES 26 A 594 LEU LEU ILE PRO ASP SER ALA LYS THR LEU PHE GLU LEU SEQRES 27 A 594 ALA ALA GLU SER ASP VAL SER THR ALA ILE ASP LEU PHE SEQRES 28 A 594 ARG GLN ALA GLY LEU GLY ASN HIS LEU SER GLY SER GLU SEQRES 29 A 594 ARG LEU THR LEU LEU ALA PRO LEU ASN SER VAL PHE LYS SEQRES 30 A 594 ASP GLY THR PRO PRO ILE ASP ALA HIS THR ARG ASN LEU SEQRES 31 A 594 LEU ARG ASN HIS ILE ILE LYS ASP GLN LEU ALA SER LYS SEQRES 32 A 594 TYR LEU TYR HIS GLY GLN THR LEU GLU THR LEU GLY GLY SEQRES 33 A 594 LYS LYS LEU ARG VAL PHE VAL TYR ARG ASN SER LEU CYS SEQRES 34 A 594 ILE GLU ASN SER CYS ILE ALA ALA HIS ASP LYS ARG GLY SEQRES 35 A 594 ARG TYR GLY THR LEU PHE THR MET ASP ARG VAL LEU THR SEQRES 36 A 594 PRO PRO MET GLY THR VAL MET ASP VAL LEU LYS GLY ASP SEQRES 37 A 594 ASN ARG PHE SER MET LEU VAL ALA ALA ILE GLN SER ALA SEQRES 38 A 594 GLY LEU THR GLU THR LEU ASN ARG GLU GLY VAL TYR THR SEQRES 39 A 594 VAL PHE ALA PRO THR ASN GLU ALA PHE ARG ALA LEU PRO SEQRES 40 A 594 PRO ARG GLU ARG SER ARG LEU LEU GLY ASP ALA LYS GLU SEQRES 41 A 594 LEU ALA ASN ILE LEU LYS TYR HIS ILE GLY ASP GLU ILE SEQRES 42 A 594 LEU VAL SER GLY GLY ILE GLY ALA LEU VAL ARG LEU LYS SEQRES 43 A 594 SER LEU GLN GLY ASP LYS LEU GLU VAL SER LEU LYS ASN SEQRES 44 A 594 ASN VAL VAL SER VAL ASN LYS GLU PRO VAL ALA GLU PRO SEQRES 45 A 594 ASP ILE MET ALA THR ASN GLY VAL VAL HIS VAL ILE THR SEQRES 46 A 594 ASN VAL LEU HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *46(H2 O) HELIX 1 AA1 ASN A 105 GLY A 114 1 10 HELIX 2 AA2 SER A 115 HIS A 124 1 10 HELIX 3 AA3 LYS A 127 GLY A 134 1 8 HELIX 4 AA4 SER A 144 SER A 150 1 7 HELIX 5 AA5 PRO A 152 SER A 161 1 10 HELIX 6 AA6 ILE A 165 HIS A 174 1 10 HELIX 7 AA7 LEU A 181 LEU A 185 5 5 HELIX 8 AA8 ASN A 242 GLU A 248 1 7 HELIX 9 AA9 GLU A 250 THR A 252 5 3 HELIX 10 AB1 PHE A 253 GLY A 264 1 12 HELIX 11 AB2 LEU A 265 GLU A 270 1 6 HELIX 12 AB3 THR A 281 GLU A 286 1 6 HELIX 13 AB4 PRO A 289 ASP A 299 1 11 HELIX 14 AB5 ASP A 299 ASN A 309 1 11 HELIX 15 AB6 CYS A 317 ILE A 321 5 5 HELIX 16 AB7 PRO A 373 LYS A 377 5 5 HELIX 17 AB8 THR A 378 ALA A 384 1 7 HELIX 18 AB9 VAL A 388 ALA A 398 1 11 HELIX 19 AC1 LEU A 400 SER A 405 1 6 HELIX 20 AC2 ASN A 417 LYS A 421 5 5 HELIX 21 AC3 ASP A 428 ASN A 437 1 10 HELIX 22 AC4 ALA A 445 LEU A 449 5 5 HELIX 23 AC5 THR A 504 GLY A 511 1 8 HELIX 24 AC6 ASP A 512 ARG A 514 5 3 HELIX 25 AC7 PHE A 515 ALA A 525 1 11 HELIX 26 AC8 THR A 543 ARG A 548 1 6 HELIX 27 AC9 PRO A 551 GLY A 560 1 10 HELIX 28 AD1 ASP A 561 HIS A 572 1 12 HELIX 29 AD2 VAL A 579 ILE A 583 5 5 SHEET 1 AA1 3 LYS A 60 THR A 63 0 SHEET 2 AA1 3 ALA A 50 VAL A 54 -1 N GLN A 52 O TYR A 61 SHEET 3 AA1 3 THR A 78 SER A 81 -1 O SER A 81 N VAL A 51 SHEET 1 AA2 7 MET A 175 VAL A 176 0 SHEET 2 AA2 7 PHE A 138 PRO A 143 -1 N THR A 139 O VAL A 176 SHEET 3 AA2 7 GLY A 227 ILE A 232 1 O HIS A 230 N ALA A 142 SHEET 4 AA2 7 ALA A 215 HIS A 223 -1 N LEU A 218 O LEU A 231 SHEET 5 AA2 7 VAL A 210 VAL A 212 -1 N VAL A 212 O ALA A 215 SHEET 6 AA2 7 ASN A 199 HIS A 204 -1 N HIS A 203 O THR A 211 SHEET 7 AA2 7 THR A 190 THR A 192 -1 N LEU A 191 O ILE A 200 SHEET 1 AA3 4 ILE A 311 LEU A 312 0 SHEET 2 AA3 4 TYR A 275 PRO A 280 -1 N THR A 276 O LEU A 312 SHEET 3 AA3 4 GLY A 362 ILE A 367 1 O ILE A 367 N ALA A 279 SHEET 4 AA3 4 ILE A 352 ALA A 359 -1 N ILE A 357 O ILE A 364 SHEET 1 AA4 3 LEU A 325 GLU A 328 0 SHEET 2 AA4 3 THR A 334 SER A 340 -1 O LEU A 335 N VAL A 327 SHEET 3 AA4 3 MET A 343 ILE A 346 -1 O THR A 345 N GLY A 338 SHEET 1 AA5 7 ILE A 439 LYS A 441 0 SHEET 2 AA5 7 LEU A 410 PRO A 415 -1 N THR A 411 O ILE A 440 SHEET 3 AA5 7 THR A 490 MET A 494 1 O PHE A 492 N LEU A 412 SHEET 4 AA5 7 SER A 477 ARG A 485 -1 N ALA A 480 O THR A 493 SHEET 5 AA5 7 LEU A 472 ILE A 474 -1 N ILE A 474 O SER A 477 SHEET 6 AA5 7 LYS A 462 VAL A 467 -1 N PHE A 466 O CYS A 473 SHEET 7 AA5 7 GLN A 453 GLU A 456 -1 N LEU A 455 O LEU A 463 SHEET 1 AA6 7 ILE A 573 GLY A 574 0 SHEET 2 AA6 7 TYR A 537 PRO A 542 -1 N THR A 538 O GLY A 574 SHEET 3 AA6 7 GLY A 623 ILE A 628 1 O HIS A 626 N VAL A 539 SHEET 4 AA6 7 GLU A 611 ALA A 620 -1 N ALA A 614 O VAL A 627 SHEET 5 AA6 7 VAL A 605 VAL A 608 -1 N VAL A 606 O VAL A 613 SHEET 6 AA6 7 LYS A 596 LYS A 602 -1 N SER A 600 O SER A 607 SHEET 7 AA6 7 LEU A 586 LYS A 590 -1 N VAL A 587 O VAL A 599 SSBOND 1 CYS A 49 CYS A 85 1555 1555 2.05 SSBOND 2 CYS A 74 CYS A 339 1555 1555 2.06 SSBOND 3 CYS A 84 CYS A 97 1555 1555 2.03 SSBOND 4 CYS A 214 CYS A 317 1555 1555 2.07 SSBOND 5 CYS A 473 CYS A 478 1555 1555 2.04 CRYST1 77.370 93.870 214.020 90.00 90.00 90.00 C 2 2 21 8 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 0.012925 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010653 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004672 0.00000