HEADER HYDROLASE 14-FEB-19 6JGT TITLE CRYSTAL STRUCTURE OF BARLEY EXOHYDROLASEI W434Y MUTANT IN COMPLEX WITH TITLE 2 METHYL 6-THIO-BETA-GENTIOBIOSIDE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-D-GLUCAN GLUCOHYDROLASE ISOENZYME EXO1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HORDEUM VULGARE SUBSP. VULGARE; SOURCE 3 ORGANISM_COMMON: DOMESTICATED BARLEY; SOURCE 4 ORGANISM_TAXID: 112509; SOURCE 5 EXPRESSION_SYSTEM: KOMAGATAELLA PASTORIS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 4922 KEYWDS BARLEY EXOHYDROLASEI, HYDROLASE, ENZYME FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR S.LUANG,V.A.STRELTSOV,M.HRMOVA REVDAT 3 29-NOV-23 6JGT 1 REMARK REVDAT 2 05-OCT-22 6JGT 1 JRNL REMARK REVDAT 1 19-AUG-20 6JGT 0 JRNL AUTH S.LUANG,X.FERNANDEZ-LUENGO,A.NIN-HILL,V.A.STRELTSOV, JRNL AUTH 2 J.G.SCHWERDT,S.ALONSO-GIL,J.R.KETUDAT CAIRNS,S.PRADEAU, JRNL AUTH 3 S.FORT,J.D.MARECHAL,L.MASGRAU,C.ROVIRA,M.HRMOVA JRNL TITL THE EVOLUTIONARY ADVANTAGE OF AN AROMATIC CLAMP IN PLANT JRNL TITL 2 FAMILY 3 GLYCOSIDE EXO-HYDROLASES. JRNL REF NAT COMMUN V. 13 5577 2022 JRNL REFN ESSN 2041-1723 JRNL PMID 36151080 JRNL DOI 10.1038/S41467-022-33180-5 REMARK 2 REMARK 2 RESOLUTION. 1.82 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) : 1.82 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.56 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 79565 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) : 0.143 REMARK 3 R VALUE (WORKING SET) : 0.142 REMARK 3 FREE R VALUE : 0.162 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4183 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) : 1.82 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5780 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.94 REMARK 3 BIN R VALUE (WORKING SET) : 0.1850 REMARK 3 BIN FREE R VALUE SET COUNT : 294 REMARK 3 BIN FREE R VALUE : 0.2180 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4594 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 156 REMARK 3 SOLVENT ATOMS : 568 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.45000 REMARK 3 B22 (A**2) : 0.45000 REMARK 3 B33 (A**2) : -0.91000 REMARK 3 B12 (A**2) : 0.00000 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): 0.079 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.077 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.046 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.819 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.962 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4760 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4602 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6419 ; 1.579 ; 1.987 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10576 ; 1.677 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 589 ; 6.196 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 192 ;38.751 ;23.646 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 768 ;13.097 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;17.061 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 725 ; 0.096 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5277 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1035 ; 0.001 ; 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): 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): 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A -3 A 357 REMARK 3 ORIGIN FOR THE GROUP (A): 24.7434 16.5439 29.4562 REMARK 3 T TENSOR REMARK 3 T11: 0.0269 T22: 0.0678 REMARK 3 T33: 0.0246 T12: 0.0117 REMARK 3 T13: 0.0199 T23: 0.0238 REMARK 3 L TENSOR REMARK 3 L11: 0.4511 L22: 0.0592 REMARK 3 L33: 0.5228 L12: -0.1365 REMARK 3 L13: -0.2146 L23: 0.0887 REMARK 3 S TENSOR REMARK 3 S11: -0.0876 S12: 0.0014 S13: -0.0587 REMARK 3 S21: 0.0368 S22: 0.0216 S23: 0.0349 REMARK 3 S31: 0.0202 S32: 0.0918 S33: 0.0660 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 358 A 373 REMARK 3 ORIGIN FOR THE GROUP (A): 11.4139 20.7827 16.0734 REMARK 3 T TENSOR REMARK 3 T11: 0.0163 T22: 0.1411 REMARK 3 T33: 0.0188 T12: 0.0110 REMARK 3 T13: -0.0049 T23: -0.0449 REMARK 3 L TENSOR REMARK 3 L11: 1.6132 L22: 1.6004 REMARK 3 L33: 1.3654 L12: -1.5634 REMARK 3 L13: -0.9062 L23: 0.7728 REMARK 3 S TENSOR REMARK 3 S11: 0.0053 S12: 0.2238 S13: -0.0953 REMARK 3 S21: 0.0193 S22: -0.1235 S23: 0.0595 REMARK 3 S31: 0.0099 S32: -0.1306 S33: 0.1181 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 374 A 602 REMARK 3 ORIGIN FOR THE GROUP (A): 2.2301 31.7843 51.2371 REMARK 3 T TENSOR REMARK 3 T11: 0.0442 T22: 0.0600 REMARK 3 T33: 0.0261 T12: 0.0141 REMARK 3 T13: -0.0008 T23: -0.0032 REMARK 3 L TENSOR REMARK 3 L11: 0.4025 L22: 0.1973 REMARK 3 L33: 0.4471 L12: -0.2745 REMARK 3 L13: -0.3076 L23: 0.1911 REMARK 3 S TENSOR REMARK 3 S11: -0.0433 S12: -0.0378 S13: 0.0068 REMARK 3 S21: 0.0202 S22: 0.0121 S23: 0.0017 REMARK 3 S31: 0.0211 S32: 0.0430 S33: 0.0312 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 6JGT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-FEB-19. REMARK 100 THE DEPOSITION ID IS D_1300011094. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-NOV-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL SI(111) REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : COLLIMATING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 79565 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.820 REMARK 200 RESOLUTION RANGE LOW (A) : 88.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 29.00 REMARK 200 R MERGE (I) : 0.09300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 38.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.82 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.87 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.84700 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: MOLREP REMARK 200 STARTING MODEL: 3WLI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.7 M AMMONIUM SULFATE, 75 MM HEPES REMARK 280 -NAOH BUFFER, PH 7, CONTAINING 7.5 MM SODIUM ACETATE AND 1.2% (W/ REMARK 280 V) PEG 400, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 90.50450 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 50.35600 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 50.35600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 135.75675 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 50.35600 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 50.35600 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 45.25225 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 50.35600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 50.35600 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 135.75675 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 50.35600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.35600 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 45.25225 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 90.50450 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 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 LYS A 603 REMARK 465 LYS A 604 REMARK 465 TYR A 605 REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 HIS A -3 REMARK 475 HIS A -2 REMARK 475 VAL A 215 REMARK 475 ASP A 216 REMARK 475 GLY A 217 REMARK 475 ILE A 218 REMARK 475 ASN A 219 REMARK 475 GLU A 220 REMARK 475 GLU A 491 REMARK 475 THR A 492 REMARK 475 LYS A 493 REMARK 475 GLY A 494 REMARK 475 ASP A 495 REMARK 475 ASN A 496 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 ND2 ASN A 466 OG1 THR A 508 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 GLU A 491 CD GLU A 491 OE2 0.107 REMARK 500 ASN A 496 C LEU A 497 N 0.237 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 HIS A -2 CA - C - N ANGL. DEV. = 33.9 DEGREES REMARK 500 HIS A -2 O - C - N ANGL. DEV. = -33.4 DEGREES REMARK 500 ALA A -1 C - N - CA ANGL. DEV. = 31.0 DEGREES REMARK 500 ARG A 126 NE - CZ - NH1 ANGL. DEV. = 5.3 DEGREES REMARK 500 ARG A 126 NE - CZ - NH2 ANGL. DEV. = -6.6 DEGREES REMARK 500 ARG A 440 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG A 440 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 VAL A 482 CG1 - CB - CG2 ANGL. DEV. = 9.7 DEGREES REMARK 500 ARG A 526 NE - CZ - NH2 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 HIS A -2 -67.19 127.81 REMARK 500 ALA A -1 139.00 -28.13 REMARK 500 ASP A 1 32.99 -96.17 REMARK 500 HIS A 98 66.07 -152.26 REMARK 500 ASP A 187 33.32 -96.12 REMARK 500 ASN A 219 146.07 85.51 REMARK 500 ASN A 221 -155.40 -121.92 REMARK 500 ILE A 225 143.23 -172.16 REMARK 500 TYR A 271 -63.31 -99.06 REMARK 500 ASP A 299 78.25 -150.05 REMARK 500 ILE A 432 -57.14 72.08 REMARK 500 THR A 442 -168.98 -160.77 REMARK 500 GLU A 491 31.34 30.34 REMARK 500 LYS A 493 -52.01 -124.88 REMARK 500 ASP A 495 147.31 56.95 REMARK 500 ASN A 496 83.26 156.22 REMARK 500 TRP A 544 -133.46 53.49 REMARK 500 VAL A 582 103.69 -47.49 REMARK 500 ASP A 584 -95.60 -58.78 REMARK 500 ALA A 585 -57.27 173.54 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 HIS A -3 HIS A -2 134.66 REMARK 500 HIS A -2 ALA A -1 144.68 REMARK 500 GLU A 491 THR A 492 144.77 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 HIS A -2 16.63 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 1PE A 708 REMARK 610 1PE A 709 REMARK 610 1PE A 710 REMARK 610 1PE A 711 REMARK 610 1PE A 712 REMARK 610 1PE A 713 REMARK 610 1PE A 714 REMARK 610 1PE A 715 REMARK 610 1PE A 716 REMARK 999 REMARK 999 SEQUENCE REMARK 999 LYS320 IS CONFIRMED BY DNA SEQUENCING RESULT. HOWEVER, THE ELECTRON REMARK 999 DENSITY MAP IS NOT CLEAR, PROBABLY SIDE CHAIN OF THIS RESIDUE IS REMARK 999 FLEXIBLE. DBREF1 6JGT A 1 605 UNP A0A287SCR5_HORVV DBREF2 6JGT A A0A287SCR5 80 684 SEQADV 6JGT HIS A -3 UNP A0A287SCR EXPRESSION TAG SEQADV 6JGT HIS A -2 UNP A0A287SCR EXPRESSION TAG SEQADV 6JGT ALA A -1 UNP A0A287SCR EXPRESSION TAG SEQADV 6JGT ALA A 0 UNP A0A287SCR EXPRESSION TAG SEQADV 6JGT LYS A 320 UNP A0A287SCR ASN 399 CONFLICT SEQADV 6JGT TYR A 434 UNP A0A287SCR TRP 513 ENGINEERED MUTATION SEQRES 1 A 609 HIS HIS ALA ALA ASP TYR VAL LEU TYR LYS ASP ALA THR SEQRES 2 A 609 LYS PRO VAL GLU ASP ARG VAL ALA ASP LEU LEU GLY ARG SEQRES 3 A 609 MET THR LEU ALA GLU LYS ILE GLY GLN MET THR GLN ILE SEQRES 4 A 609 GLU ARG LEU VAL ALA THR PRO ASP VAL LEU ARG ASP ASN SEQRES 5 A 609 PHE ILE GLY SER LEU LEU SER GLY GLY GLY SER VAL PRO SEQRES 6 A 609 ARG LYS GLY ALA THR ALA LYS GLU TRP GLN ASP MET VAL SEQRES 7 A 609 ASP GLY PHE GLN LYS ALA CYS MET SER THR ARG LEU GLY SEQRES 8 A 609 ILE PRO MET ILE TYR GLY ILE ASP ALA VAL HIS GLY GLN SEQRES 9 A 609 ASN ASN VAL TYR GLY ALA THR ILE PHE PRO HIS ASN VAL SEQRES 10 A 609 GLY LEU GLY ALA THR ARG ASP PRO TYR LEU VAL LYS ARG SEQRES 11 A 609 ILE GLY GLU ALA THR ALA LEU GLU VAL ARG ALA THR GLY SEQRES 12 A 609 ILE GLN TYR ALA PHE ALA PRO CYS ILE ALA VAL CYS ARG SEQRES 13 A 609 ASP PRO ARG TRP GLY ARG CYS TYR GLU SER TYR SER GLU SEQRES 14 A 609 ASP ARG ARG ILE VAL GLN SER MET THR GLU LEU ILE PRO SEQRES 15 A 609 GLY LEU GLN GLY ASP VAL PRO LYS ASP PHE THR SER GLY SEQRES 16 A 609 MET PRO PHE VAL ALA GLY LYS ASN LYS VAL ALA ALA CYS SEQRES 17 A 609 ALA LYS HIS PHE VAL GLY ASP GLY GLY THR VAL ASP GLY SEQRES 18 A 609 ILE ASN GLU ASN ASN THR ILE ILE ASN ARG GLU GLY LEU SEQRES 19 A 609 MET ASN ILE HIS MET PRO ALA TYR LYS ASN ALA MET ASP SEQRES 20 A 609 LYS GLY VAL SER THR VAL MET ILE SER TYR SER SER TRP SEQRES 21 A 609 ASN GLY VAL LYS MET HIS ALA ASN GLN ASP LEU VAL THR SEQRES 22 A 609 GLY TYR LEU LYS ASP THR LEU LYS PHE LYS GLY PHE VAL SEQRES 23 A 609 ILE SER ASP TRP GLU GLY ILE ASP ARG ILE THR THR PRO SEQRES 24 A 609 ALA GLY SER ASP TYR SER TYR SER VAL LYS ALA SER ILE SEQRES 25 A 609 LEU ALA GLY LEU ASP MET ILE MET VAL PRO ASN LYS TYR SEQRES 26 A 609 GLN GLN PHE ILE SER ILE LEU THR GLY HIS VAL ASN GLY SEQRES 27 A 609 GLY VAL ILE PRO MET SER ARG ILE ASP ASP ALA VAL THR SEQRES 28 A 609 ARG ILE LEU ARG VAL LYS PHE THR MET GLY LEU PHE GLU SEQRES 29 A 609 ASN PRO TYR ALA ASP PRO ALA MET ALA GLU GLN LEU GLY SEQRES 30 A 609 LYS GLN GLU HIS ARG ASP LEU ALA ARG GLU ALA ALA ARG SEQRES 31 A 609 LYS SER LEU VAL LEU LEU LYS ASN GLY LYS THR SER THR SEQRES 32 A 609 ASP ALA PRO LEU LEU PRO LEU PRO LYS LYS ALA PRO LYS SEQRES 33 A 609 ILE LEU VAL ALA GLY SER HIS ALA ASP ASN LEU GLY TYR SEQRES 34 A 609 GLN CYS GLY GLY TRP THR ILE GLU TYR GLN GLY ASP THR SEQRES 35 A 609 GLY ARG THR THR VAL GLY THR THR ILE LEU GLU ALA VAL SEQRES 36 A 609 LYS ALA ALA VAL ASP PRO SER THR VAL VAL VAL PHE ALA SEQRES 37 A 609 GLU ASN PRO ASP ALA GLU PHE VAL LYS SER GLY GLY PHE SEQRES 38 A 609 SER TYR ALA ILE VAL ALA VAL GLY GLU HIS PRO TYR THR SEQRES 39 A 609 GLU THR LYS GLY ASP ASN LEU ASN LEU THR ILE PRO GLU SEQRES 40 A 609 PRO GLY LEU SER THR VAL GLN ALA VAL CYS GLY GLY VAL SEQRES 41 A 609 ARG CYS ALA THR VAL LEU ILE SER GLY ARG PRO VAL VAL SEQRES 42 A 609 VAL GLN PRO LEU LEU ALA ALA SER ASP ALA LEU VAL ALA SEQRES 43 A 609 ALA TRP LEU PRO GLY SER GLU GLY GLN GLY VAL THR ASP SEQRES 44 A 609 ALA LEU PHE GLY ASP PHE GLY PHE THR GLY ARG LEU PRO SEQRES 45 A 609 ARG THR TRP PHE LYS SER VAL ASP GLN LEU PRO MET ASN SEQRES 46 A 609 VAL GLY ASP ALA HIS TYR ASP PRO LEU PHE ARG LEU GLY SEQRES 47 A 609 TYR GLY LEU THR THR ASN ALA THR LYS LYS TYR MODRES 6JGT NAG A 701 NAG -D HET U1Y B 1 13 HET BGC B 2 11 HET NAG A 701 14 HET GOL A 703 6 HET GOL A 704 6 HET GOL A 705 6 HET GOL A 706 6 HET GOL A 707 6 HET 1PE A 708 5 HET 1PE A 709 10 HET 1PE A 710 8 HET 1PE A 711 5 HET 1PE A 712 5 HET 1PE A 713 7 HET 1PE A 714 8 HET 1PE A 715 5 HET 1PE A 716 6 HET ACT A 717 4 HET ACT A 718 4 HET ACT A 719 4 HET ACT A 720 4 HET ACT A 721 4 HET ACT A 722 4 HET SO4 A 723 5 HETNAM U1Y METHYL 6-THIO-BETA-D-GLUCOPYRANOSIDE HETNAM BGC BETA-D-GLUCOPYRANOSE HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM GOL GLYCEROL HETNAM 1PE PENTAETHYLENE GLYCOL HETNAM ACT ACETATE ION HETNAM SO4 SULFATE ION HETSYN BGC BETA-D-GLUCOSE; D-GLUCOSE; GLUCOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN 1PE PEG400 FORMUL 2 U1Y C7 H14 O5 S FORMUL 2 BGC C6 H12 O6 FORMUL 3 NAG C8 H15 N O6 FORMUL 4 GOL 5(C3 H8 O3) FORMUL 9 1PE 9(C10 H22 O6) FORMUL 18 ACT 6(C2 H3 O2 1-) FORMUL 24 SO4 O4 S 2- FORMUL 25 HOH *568(H2 O) HELIX 1 AA1 VAL A 3 ASP A 7 5 5 HELIX 2 AA2 PRO A 11 GLY A 21 1 11 HELIX 3 AA3 THR A 24 MET A 32 1 9 HELIX 4 AA4 LEU A 38 ALA A 40 5 3 HELIX 5 AA5 THR A 41 ASN A 48 1 8 HELIX 6 AA6 THR A 66 SER A 83 1 18 HELIX 7 AA7 HIS A 111 ARG A 119 1 9 HELIX 8 AA8 ASP A 120 THR A 138 1 19 HELIX 9 AA9 ARG A 158 SER A 162 5 5 HELIX 10 AB1 ASP A 166 THR A 174 1 9 HELIX 11 AB2 GLU A 175 GLY A 182 1 8 HELIX 12 AB3 GLY A 210 ILE A 218 5 9 HELIX 13 AB4 ASN A 226 ILE A 233 1 8 HELIX 14 AB5 MET A 235 LYS A 244 1 10 HELIX 15 AB6 ASN A 264 THR A 269 1 6 HELIX 16 AB7 ILE A 289 THR A 293 5 5 HELIX 17 AB8 ASP A 299 GLY A 311 1 13 HELIX 18 AB9 LYS A 320 GLY A 334 1 15 HELIX 19 AC1 PRO A 338 MET A 356 1 19 HELIX 20 AC2 ASP A 365 LEU A 372 5 8 HELIX 21 AC3 LYS A 374 LEU A 389 1 16 HELIX 22 AC4 ASN A 422 GLY A 428 1 7 HELIX 23 AC5 THR A 446 VAL A 455 1 10 HELIX 24 AC6 ASP A 468 GLY A 475 1 8 HELIX 25 AC7 GLY A 505 GLY A 514 1 10 HELIX 26 AC8 VAL A 530 SER A 537 1 8 HELIX 27 AC9 GLY A 550 PHE A 558 1 9 HELIX 28 AD1 SER A 574 LEU A 578 5 5 SHEET 1 AA1 5 TYR A 142 ALA A 143 0 SHEET 2 AA1 5 ILE A 91 ILE A 94 1 N ILE A 94 O TYR A 142 SHEET 3 AA1 5 SER A 52 SER A 55 1 N LEU A 53 O GLY A 93 SHEET 4 AA1 5 THR A 33 GLU A 36 1 N ILE A 35 O SER A 52 SHEET 5 AA1 5 ILE A 315 MET A 316 1 O ILE A 315 N GLN A 34 SHEET 1 AA2 3 CYS A 204 PHE A 208 0 SHEET 2 AA2 3 THR A 248 ILE A 251 1 O MET A 250 N PHE A 208 SHEET 3 AA2 3 PHE A 281 ILE A 283 1 O ILE A 283 N VAL A 249 SHEET 1 AA3 3 ASN A 222 THR A 223 0 SHEET 2 AA3 3 SER A 255 TRP A 256 1 O SER A 255 N THR A 223 SHEET 3 AA3 3 VAL A 259 LYS A 260 -1 O VAL A 259 N TRP A 256 SHEET 1 AA4 6 VAL A 390 ASN A 394 0 SHEET 2 AA4 6 ALA A 539 TRP A 544 -1 O ALA A 542 N VAL A 390 SHEET 3 AA4 6 CYS A 518 ILE A 523 1 N LEU A 522 O VAL A 541 SHEET 4 AA4 6 ALA A 480 GLY A 485 1 N VAL A 482 O VAL A 521 SHEET 5 AA4 6 LYS A 412 ALA A 416 1 N ALA A 416 O ALA A 483 SHEET 6 AA4 6 VAL A 460 ALA A 464 1 O VAL A 462 N VAL A 415 SSBOND 1 CYS A 151 CYS A 159 1555 1555 2.15 SSBOND 2 CYS A 513 CYS A 518 1555 1555 2.01 LINK ND2 ASN A 600 C1 NAG A 701 1555 1555 1.45 LINK S6 U1Y B 1 C1 BGC B 2 1555 1555 1.76 CISPEP 1 ALA A 145 PRO A 146 0 6.02 CISPEP 2 LYS A 206 HIS A 207 0 -8.19 CISPEP 3 PHE A 208 VAL A 209 0 -4.12 CISPEP 4 THR A 294 PRO A 295 0 -7.21 CISPEP 5 VAL A 317 PRO A 318 0 -10.58 CISPEP 6 LEU A 404 PRO A 405 0 2.57 CISPEP 7 GLU A 503 PRO A 504 0 -1.64 CISPEP 8 LEU A 578 PRO A 579 0 -2.16 CRYST1 100.712 100.712 181.009 90.00 90.00 90.00 P 43 21 2 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 0.009929 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009929 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005525 0.00000