HEADER SUGAR BINDING PROTEIN 10-JUN-15 5BY3 TITLE A NOVEL FAMILY GH115 4-O-METHYL-ALPHA-GLUCURONIDASE, BTGH115A, WITH TITLE 2 SPECIFICITY FOR DECORATED ARABINOGALACTANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: BTGH115A; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACTEROIDES THETAIOTAOMICRON (STRAIN ATCC 29148 SOURCE 3 / DSM 2079 / NCTC 10582 / E50 / VPI-5482); SOURCE 4 ORGANISM_TAXID: 226186; SOURCE 5 GENE: BT_2958; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GLYCOSIDE, HYDROLASE, ARABINOGALACTANS ALPHA-GLUCURONIDASE, SUGAR KEYWDS 2 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.LAMMERTS VAN BUEREN,G.J.DAVIES,J.P.TURKENBURG REVDAT 3 09-DEC-15 5BY3 1 JRNL REVDAT 2 05-AUG-15 5BY3 1 JRNL REVDAT 1 22-JUL-15 5BY3 0 JRNL AUTH F.AALBERS,J.P.TURKENBURG,G.J.DAVIES,L.DIJKHUIZEN, JRNL AUTH 2 A.LAMMERTS VAN BUEREN JRNL TITL STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF A NOVEL FAMILY JRNL TITL 2 GH115 4-O-METHYL-ALPHA-GLUCURONIDASE WITH SPECIFICITY FOR JRNL TITL 3 DECORATED ARABINOGALACTANS. JRNL REF J.MOL.BIOL. V. 427 3935 2015 JRNL REFN ESSN 1089-8638 JRNL PMID 26186997 JRNL DOI 10.1016/J.JMB.2015.07.006 REMARK 2 REMARK 2 RESOLUTION. 2.44 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0103 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.44 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 30528 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) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1630 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) : 2.44 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.51 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2231 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.87 REMARK 3 BIN R VALUE (WORKING SET) : 0.2860 REMARK 3 BIN FREE R VALUE SET COUNT : 110 REMARK 3 BIN FREE R VALUE : 0.3590 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6064 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 99 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.57000 REMARK 3 B22 (A**2) : -3.17000 REMARK 3 B33 (A**2) : -0.40000 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): 0.487 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.298 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.239 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.658 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.910 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6224 ; 0.013 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8427 ; 1.848 ; 1.958 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 764 ; 7.394 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 297 ;38.887 ;24.276 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1040 ;19.244 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;20.359 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 905 ; 0.130 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4723 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3041 ; 4.225 ; 5.274 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3801 ; 6.251 ; 7.901 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3183 ; 4.884 ; 5.406 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): 9404 ; 9.417 ;43.134 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5BY3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JUN-15. REMARK 100 THE DEPOSITION ID IS D_1000210686. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-FEB-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 3.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795, 0.9798, 0.9682 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 : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32214 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.440 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.44 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.51 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.61400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350 0.2M SODIUM SULFATE 0.01M REMARK 280 GLYCINE, PH 3.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 33.88500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.20000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.15000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 61.20000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.88500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 51.15000 REMARK 290 SMTRY3 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL 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 MSE A 1 REMARK 465 ALA A 2 REMARK 465 HIS A 3 REMARK 465 HIS A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 HIS A 8 REMARK 465 SER A 9 REMARK 465 ALA A 10 REMARK 465 ALA A 11 REMARK 465 LEU A 12 REMARK 465 GLU A 13 REMARK 465 VAL A 14 REMARK 465 LEU A 15 REMARK 465 PHE A 16 REMARK 465 GLN A 17 REMARK 465 LYS A 18 REMARK 465 ARG A 778 REMARK 465 ASN A 779 REMARK 465 SER A 780 REMARK 465 SER A 781 REMARK 465 GLY A 782 REMARK 465 ILE A 783 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 O PRO A 246 O THR A 291 2.17 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 163 CG - CD - NE ANGL. DEV. = -13.1 DEGREES REMARK 500 ARG A 198 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 198 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 207 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 MSE A 247 C - N - CA ANGL. DEV. = -31.0 DEGREES REMARK 500 MSE A 569 CG - SE - CE ANGL. DEV. = 15.4 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 ASN A 64 -63.66 -122.08 REMARK 500 ILE A 73 122.65 -21.51 REMARK 500 GLN A 75 -6.91 -146.40 REMARK 500 GLN A 75 -12.96 -143.88 REMARK 500 SER A 87 -47.68 -173.23 REMARK 500 ASN A 91 75.01 37.44 REMARK 500 ASN A 91 76.28 35.43 REMARK 500 GLU A 133 -57.38 -27.88 REMARK 500 ARG A 153 -6.63 -142.54 REMARK 500 GLU A 154 129.98 -1.38 REMARK 500 MSE A 215 8.19 -154.90 REMARK 500 ALA A 248 23.79 46.10 REMARK 500 ASN A 268 24.33 -144.95 REMARK 500 ARG A 295 -147.77 -126.44 REMARK 500 HIS A 298 -107.78 -120.91 REMARK 500 LYS A 345 -120.67 48.30 REMARK 500 ASN A 369 -10.72 80.16 REMARK 500 ILE A 437 -71.70 69.49 REMARK 500 PRO A 439 58.15 -117.31 REMARK 500 ASN A 453 87.84 -153.89 REMARK 500 LEU A 474 -151.40 -97.93 REMARK 500 ARG A 496 116.21 -170.28 REMARK 500 ASN A 608 -73.93 77.64 REMARK 500 ARG A 613 -14.58 78.88 REMARK 500 ARG A 620 11.77 59.98 REMARK 500 THR A 634 -62.88 -91.66 REMARK 500 LYS A 653 -105.55 -78.33 REMARK 500 GLU A 661 -70.26 -31.97 REMARK 500 SER A 667 18.21 58.53 REMARK 500 THR A 687 152.37 55.64 REMARK 500 PRO A 698 46.11 -76.41 REMARK 500 LEU A 707 87.46 39.80 REMARK 500 ALA A 716 31.53 -72.11 REMARK 500 GLU A 717 107.44 71.62 REMARK 500 ARG A 728 65.99 -106.70 REMARK 500 LYS A 753 -30.70 101.61 REMARK 500 GLU A 764 -81.34 -56.48 REMARK 500 TYR A 774 118.17 52.93 REMARK 500 GLU A 775 -85.72 -55.95 REMARK 500 VAL A 776 151.75 64.54 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 GLY A 461 VAL A 462 140.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 802 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 404 O REMARK 620 2 ASP A 436 OD2 148.2 REMARK 620 3 HOH A 952 O 108.6 77.3 REMARK 620 4 HOH A 973 O 74.4 75.6 81.9 REMARK 620 5 HOH A 905 O 74.8 94.1 168.7 88.8 REMARK 620 6 HOH A 959 O 130.6 78.2 94.9 153.6 90.6 REMARK 620 N 1 2 3 4 5 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 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 802 DBREF 5BY3 A 17 783 UNP Q8A3J6 Q8A3J6_BACTN 23 789 SEQADV 5BY3 MSE A 1 UNP Q8A3J6 INITIATING METHIONINE SEQADV 5BY3 ALA A 2 UNP Q8A3J6 EXPRESSION TAG SEQADV 5BY3 HIS A 3 UNP Q8A3J6 EXPRESSION TAG SEQADV 5BY3 HIS A 4 UNP Q8A3J6 EXPRESSION TAG SEQADV 5BY3 HIS A 5 UNP Q8A3J6 EXPRESSION TAG SEQADV 5BY3 HIS A 6 UNP Q8A3J6 EXPRESSION TAG SEQADV 5BY3 HIS A 7 UNP Q8A3J6 EXPRESSION TAG SEQADV 5BY3 HIS A 8 UNP Q8A3J6 EXPRESSION TAG SEQADV 5BY3 SER A 9 UNP Q8A3J6 EXPRESSION TAG SEQADV 5BY3 ALA A 10 UNP Q8A3J6 EXPRESSION TAG SEQADV 5BY3 ALA A 11 UNP Q8A3J6 EXPRESSION TAG SEQADV 5BY3 LEU A 12 UNP Q8A3J6 EXPRESSION TAG SEQADV 5BY3 GLU A 13 UNP Q8A3J6 EXPRESSION TAG SEQADV 5BY3 VAL A 14 UNP Q8A3J6 EXPRESSION TAG SEQADV 5BY3 LEU A 15 UNP Q8A3J6 EXPRESSION TAG SEQADV 5BY3 PHE A 16 UNP Q8A3J6 EXPRESSION TAG SEQRES 1 A 783 MSE ALA HIS HIS HIS HIS HIS HIS SER ALA ALA LEU GLU SEQRES 2 A 783 VAL LEU PHE GLN LYS ASP PHE VAL LEU GLN SER GLY GLN SEQRES 3 A 783 PRO VAL ALA ILE ALA CYS SER GLY SER GLU ALA PRO VAL SEQRES 4 A 783 VAL ARG THR SER LEU ASP LEU LEU SER ARG ASP LEU GLN SEQRES 5 A 783 THR VAL LEU SER ALA THR ALA HIS ILE ASP THR ASN THR SEQRES 6 A 783 GLY ASN ILE ILE VAL GLY THR ILE GLY GLN SER LYS LEU SEQRES 7 A 783 ILE GLU GLN ALA GLY ILE ASP ILE SER ALA LEU LYS ASN SEQRES 8 A 783 LYS LYS GLN ALA PHE MSE LEU ALA VAL SER GLU ASP GLY SEQRES 9 A 783 LYS LEU VAL VAL ALA GLY SER ASP SER HIS GLY THR ALA SEQRES 10 A 783 TYR GLY ILE LEU GLU ILE SER ARG LEU LEU GLY VAL SER SEQRES 11 A 783 PRO TRP GLU TRP TRP ALA ASP VAL THR PRO GLU LYS LYS SEQRES 12 A 783 GLU THR PHE ARG LEU SER GLY LYS PHE ARG GLU LEU GLN SEQRES 13 A 783 SER PRO SER VAL GLU TYR ARG GLY ILE PHE ILE ASN ASP SEQRES 14 A 783 GLU ASP TRP GLY LEU MSE PRO TRP SER ASN LYS THR TYR SEQRES 15 A 783 GLU PRO SER ASP VAL LYS GLY GLU ILE GLY PRO ARG THR SEQRES 16 A 783 ASN GLU ARG ILE PHE GLU LEU LEU LEU ARG LEU ARG ALA SEQRES 17 A 783 ASN THR TYR TRP PRO ALA MSE HIS GLU CYS THR LEU PRO SEQRES 18 A 783 PHE PHE LEU THR LYS GLY ASN ARG GLU ALA ALA LYS LYS SEQRES 19 A 783 TYR GLY ILE PHE MSE GLY ALA SER HIS CYS GLU PRO MSE SEQRES 20 A 783 ALA CYS ASN ALA ALA GLY GLU TRP LYS ILE ARG GLY LYS SEQRES 21 A 783 GLY ALA TYR ASP TYR VAL ASN ASN SER PRO ALA VAL TYR SEQRES 22 A 783 GLN PHE TRP GLU ASP ARG VAL LYS GLU VAL ALA GLY GLN SEQRES 23 A 783 GLU ILE LEU TYR THR LEU GLY MSE ARG GLY VAL HIS ASP SEQRES 24 A 783 GLY LYS MSE GLN GLY ALA LYS THR VAL GLU GLU GLN LYS SEQRES 25 A 783 ALA VAL LEU ASP ARG VAL PHE VAL ASP GLN ARG GLY LEU SEQRES 26 A 783 LEU GLU LYS TYR VAL ASN LYS ASP VAL THR GLN VAL PRO SEQRES 27 A 783 GLN VAL PHE ILE PRO TYR LYS GLU VAL LEU ASP ILE TYR SEQRES 28 A 783 HIS ALA GLY LEU GLN VAL PRO GLU ASP VAL THR LEU MSE SEQRES 29 A 783 TRP CYS ASP ASP ASN TYR GLY TYR ILE ARG HIS PHE PRO SEQRES 30 A 783 THR ALA GLU GLU ARG ALA ARG LYS GLY GLY ASN GLY VAL SEQRES 31 A 783 TYR TYR HIS VAL SER TYR TRP GLY ARG PRO HIS ASP HIS SEQRES 32 A 783 LEU TRP LEU SER THR MSE SER PRO SER LEU ILE TYR GLN SEQRES 33 A 783 GLN MSE LYS GLN ALA TYR ASP GLN GLY ILE GLN LYS MSE SEQRES 34 A 783 TRP ILE LEU ASN VAL GLY ASP ILE LYS PRO ALA GLU TYR SEQRES 35 A 783 GLN ILE GLU LEU PHE MSE ASP MSE ALA TRP ASN LEU ASP SEQRES 36 A 783 LYS VAL SER SER GLU GLY VAL THR ALA HIS LEU LYS HIS SEQRES 37 A 783 TRP LEU GLU ARG GLU LEU GLY THR SER CYS ALA LYS THR SEQRES 38 A 783 ILE LEU SER VAL MSE GLN GLU HIS TYR ARG LEU ALA HIS SEQRES 39 A 783 ILE ARG LYS PRO GLU PHE MSE GLY ASN THR ARG GLU GLU SEQRES 40 A 783 GLU LYS ASN PRO VAL TYR ARG VAL VAL LYS ASP LEU PRO SEQRES 41 A 783 TRP SER GLU ARG GLU ILE ASN GLU ARG LEU ASN ALA TYR SEQRES 42 A 783 SER GLU LEU SER GLU THR VAL GLU LYS ALA ALA SER LYS SEQRES 43 A 783 VAL PRO ALA GLY ARG GLN SER ALA TYR PHE GLU LEU VAL SEQRES 44 A 783 LYS TYR PRO VAL GLN ALA ALA THR GLN MSE ASN ARG LYS SEQRES 45 A 783 LEU LEU TYR ALA GLN LEU ALA ARG HIS ASP LYS GLU ASP SEQRES 46 A 783 TRP GLU LYS SER ASP ALA ALA TYR ASP SER ILE ALA ALA SEQRES 47 A 783 LEU THR GLN HIS TYR ASN SER LEU GLU ASN GLY LYS TRP SEQRES 48 A 783 ASN ARG MSE MSE ASP PHE LYS PRO ARG LYS LEU PRO VAL SEQRES 49 A 783 PHE ASN ARG VAL GLU ARG LYS ALA ALA THR ALA PRO MSE SEQRES 50 A 783 THR ALA ASP ARG LYS ALA VAL CYS GLN TRP ASN ALA ALA SEQRES 51 A 783 GLU ALA LYS LYS GLY ASN ALA ILE VAL CYS GLU GLY LEU SEQRES 52 A 783 GLY TYR GLU SER LYS ALA ALA GLU ILE LYS LYS GLY ASP SEQRES 53 A 783 ALA LEU THR PHE SER PHE GLY ASN LEU LYS THR ASP SER SEQRES 54 A 783 VAL GLU VAL ASP ILE ARG LEU LEU PRO ASN HIS PRO VAL SEQRES 55 A 783 HIS GLY ASP LYS LEU ARG PHE THR VAL SER LEU ASP GLY SEQRES 56 A 783 ALA GLU PRO GLU VAL ILE ALA TYR GLU THR LYS GLY ARG SEQRES 57 A 783 SER GLU GLU TRP LYS GLU ASN VAL LEU ARG ASN GLN ALA SEQRES 58 A 783 ILE ARG LYS ILE VAL LEU PRO VAL THR GLY LYS LYS SER SEQRES 59 A 783 HIS GLN LEU VAL ILE LYS ALA LEU ASP GLU GLY VAL ILE SEQRES 60 A 783 LEU ASP GLN VAL MSE LEU TYR GLU VAL ASN ARG ASN SER SEQRES 61 A 783 SER GLY ILE MODRES 5BY3 MSE A 97 MET MODIFIED RESIDUE MODRES 5BY3 MSE A 175 MET MODIFIED RESIDUE MODRES 5BY3 MSE A 215 MET MODIFIED RESIDUE MODRES 5BY3 MSE A 239 MET MODIFIED RESIDUE MODRES 5BY3 MSE A 247 MET MODIFIED RESIDUE MODRES 5BY3 MSE A 294 MET MODIFIED RESIDUE MODRES 5BY3 MSE A 302 MET MODIFIED RESIDUE MODRES 5BY3 MSE A 364 MET MODIFIED RESIDUE MODRES 5BY3 MSE A 409 MET MODIFIED RESIDUE MODRES 5BY3 MSE A 418 MET MODIFIED RESIDUE MODRES 5BY3 MSE A 429 MET MODIFIED RESIDUE MODRES 5BY3 MSE A 448 MET MODIFIED RESIDUE MODRES 5BY3 MSE A 450 MET MODIFIED RESIDUE MODRES 5BY3 MSE A 486 MET MODIFIED RESIDUE MODRES 5BY3 MSE A 501 MET MODIFIED RESIDUE MODRES 5BY3 MSE A 569 MET MODIFIED RESIDUE MODRES 5BY3 MSE A 614 MET MODIFIED RESIDUE MODRES 5BY3 MSE A 615 MET MODIFIED RESIDUE MODRES 5BY3 MSE A 637 MET MODIFIED RESIDUE MODRES 5BY3 MSE A 772 MET MODIFIED RESIDUE HET MSE A 97 8 HET MSE A 175 8 HET MSE A 215 8 HET MSE A 239 8 HET MSE A 247 8 HET MSE A 294 8 HET MSE A 302 8 HET MSE A 364 8 HET MSE A 409 8 HET MSE A 418 8 HET MSE A 429 8 HET MSE A 448 8 HET MSE A 450 8 HET MSE A 486 8 HET MSE A 501 8 HET MSE A 569 8 HET MSE A 614 8 HET MSE A 615 8 HET MSE A 637 8 HET MSE A 772 8 HET SO4 A 801 5 HET NI A 802 1 HETNAM MSE SELENOMETHIONINE HETNAM SO4 SULFATE ION HETNAM NI NICKEL (II) ION FORMUL 1 MSE 20(C5 H11 N O2 SE) FORMUL 2 SO4 O4 S 2- FORMUL 3 NI NI 2+ FORMUL 4 HOH *99(H2 O) HELIX 1 AA1 ALA A 37 SER A 56 1 20 HELIX 2 AA2 SER A 76 ALA A 82 1 7 HELIX 3 AA3 ASP A 112 LEU A 127 1 16 HELIX 4 AA4 ASP A 169 TRP A 172 5 4 HELIX 5 AA5 GLY A 173 THR A 181 1 9 HELIX 6 AA6 GLY A 192 LEU A 206 1 15 HELIX 7 AA7 PRO A 221 THR A 225 5 5 HELIX 8 AA8 GLY A 227 GLY A 236 1 10 HELIX 9 AA9 ASN A 250 GLY A 259 1 10 HELIX 10 AB1 ASP A 264 ALA A 284 1 21 HELIX 11 AB2 THR A 307 VAL A 330 1 24 HELIX 12 AB3 ASP A 333 VAL A 337 5 5 HELIX 13 AB4 GLU A 346 ALA A 353 1 8 HELIX 14 AB5 THR A 378 ARG A 384 1 7 HELIX 15 AB6 SER A 410 GLN A 424 1 15 HELIX 16 AB7 ALA A 440 ASN A 453 1 14 HELIX 17 AB8 ASN A 453 GLU A 460 1 8 HELIX 18 AB9 GLY A 461 LEU A 474 1 14 HELIX 19 AC1 GLY A 475 ARG A 496 1 22 HELIX 20 AC2 LYS A 497 MSE A 501 5 5 HELIX 21 AC3 ASN A 510 VAL A 515 5 6 HELIX 22 AC4 SER A 522 ALA A 544 1 23 HELIX 23 AC5 SER A 545 VAL A 547 5 3 HELIX 24 AC6 PRO A 548 GLY A 550 5 3 HELIX 25 AC7 ARG A 551 VAL A 559 1 9 HELIX 26 AC8 VAL A 559 HIS A 581 1 23 HELIX 27 AC9 TRP A 586 ASN A 604 1 19 HELIX 28 AD1 LYS A 618 ASN A 626 5 9 HELIX 29 AD2 SER A 729 ASN A 739 1 11 SHEET 1 AA1 2 PHE A 20 GLN A 23 0 SHEET 2 AA1 2 THR A 145 LEU A 148 -1 O PHE A 146 N LEU A 22 SHEET 1 AA2 6 ALA A 59 ASP A 62 0 SHEET 2 AA2 6 VAL A 28 ALA A 31 1 N ILE A 30 O HIS A 60 SHEET 3 AA2 6 ILE A 68 THR A 72 1 O VAL A 70 N ALA A 31 SHEET 4 AA2 6 LEU A 106 GLY A 110 1 O VAL A 108 N GLY A 71 SHEET 5 AA2 6 PHE A 96 VAL A 100 -1 N ALA A 99 O VAL A 107 SHEET 6 AA2 6 LEU A 155 GLN A 156 -1 O GLN A 156 N PHE A 96 SHEET 1 AA3 8 PHE A 238 MSE A 239 0 SHEET 2 AA3 8 THR A 210 TRP A 212 1 N TYR A 211 O PHE A 238 SHEET 3 AA3 8 TYR A 162 PHE A 166 1 N ILE A 165 O TRP A 212 SHEET 4 AA3 8 MSE A 429 ASN A 433 1 O TRP A 430 N TYR A 162 SHEET 5 AA3 8 ASN A 388 HIS A 393 1 N TYR A 392 O ASN A 433 SHEET 6 AA3 8 THR A 362 CYS A 366 1 N LEU A 363 O GLY A 389 SHEET 7 AA3 8 GLN A 339 PHE A 341 1 N PHE A 341 O MSE A 364 SHEET 8 AA3 8 TYR A 290 THR A 291 1 N TYR A 290 O VAL A 340 SHEET 1 AA4 4 GLN A 646 TRP A 647 0 SHEET 2 AA4 4 VAL A 766 MSE A 772 -1 O VAL A 771 N TRP A 647 SHEET 3 AA4 4 ALA A 670 ILE A 672 -1 N ALA A 670 O LEU A 768 SHEET 4 AA4 4 ILE A 658 VAL A 659 -1 N ILE A 658 O GLU A 671 SHEET 1 AA5 4 GLN A 646 TRP A 647 0 SHEET 2 AA5 4 VAL A 766 MSE A 772 -1 O VAL A 771 N TRP A 647 SHEET 3 AA5 4 SER A 689 LEU A 696 -1 N ARG A 695 O GLN A 770 SHEET 4 AA5 4 ALA A 741 PRO A 748 -1 O ILE A 745 N VAL A 692 SHEET 1 AA6 4 ALA A 677 PHE A 682 0 SHEET 2 AA6 4 HIS A 755 ALA A 761 -1 O LEU A 757 N PHE A 680 SHEET 3 AA6 4 ARG A 708 LEU A 713 -1 N SER A 712 O VAL A 758 SHEET 4 AA6 4 GLU A 719 ALA A 722 -1 O ILE A 721 N PHE A 709 LINK C PHE A 96 N MSE A 97 1555 1555 1.34 LINK C MSE A 97 N LEU A 98 1555 1555 1.33 LINK C LEU A 174 N MSE A 175 1555 1555 1.34 LINK C MSE A 175 N PRO A 176 1555 1555 1.35 LINK C ALA A 214 N MSE A 215 1555 1555 1.32 LINK C MSE A 215 N HIS A 216 1555 1555 1.32 LINK C PHE A 238 N MSE A 239 1555 1555 1.33 LINK C MSE A 239 N GLY A 240 1555 1555 1.33 LINK C PRO A 246 N MSE A 247 1555 1555 1.35 LINK C MSE A 247 N ALA A 248 1555 1555 1.33 LINK C GLY A 293 N MSE A 294 1555 1555 1.33 LINK C MSE A 294 N ARG A 295 1555 1555 1.34 LINK C LYS A 301 N MSE A 302 1555 1555 1.33 LINK C MSE A 302 N GLN A 303 1555 1555 1.33 LINK C LEU A 363 N MSE A 364 1555 1555 1.33 LINK C MSE A 364 N TRP A 365 1555 1555 1.32 LINK O LEU A 404 NI NI A 802 1555 1555 2.37 LINK C THR A 408 N MSE A 409 1555 1555 1.33 LINK C MSE A 409 N SER A 410 1555 1555 1.32 LINK C GLN A 417 N MSE A 418 1555 1555 1.33 LINK C MSE A 418 N LYS A 419 1555 1555 1.33 LINK C LYS A 428 N MSE A 429 1555 1555 1.33 LINK C MSE A 429 N TRP A 430 1555 1555 1.34 LINK OD2 ASP A 436 NI NI A 802 1555 1555 2.40 LINK C PHE A 447 N MSE A 448 1555 1555 1.33 LINK C MSE A 448 N ASP A 449 1555 1555 1.34 LINK C ASP A 449 N MSE A 450 1555 1555 1.34 LINK C MSE A 450 N ALA A 451 1555 1555 1.32 LINK C VAL A 485 N MSE A 486 1555 1555 1.34 LINK C MSE A 486 N GLN A 487 1555 1555 1.33 LINK C PHE A 500 N MSE A 501 1555 1555 1.33 LINK C MSE A 501 N GLY A 502 1555 1555 1.34 LINK C GLN A 568 N MSE A 569 1555 1555 1.34 LINK C MSE A 569 N ASN A 570 1555 1555 1.34 LINK C ARG A 613 N MSE A 614 1555 1555 1.34 LINK C MSE A 614 N MSE A 615 1555 1555 1.34 LINK C MSE A 615 N ASP A 616 1555 1555 1.33 LINK C PRO A 636 N MSE A 637 1555 1555 1.35 LINK C MSE A 637 N THR A 638 1555 1555 1.33 LINK C VAL A 771 N MSE A 772 1555 1555 1.34 LINK C MSE A 772 N LEU A 773 1555 1555 1.33 LINK NI NI A 802 O HOH A 952 1555 1555 2.77 LINK NI NI A 802 O HOH A 973 1555 1555 2.49 LINK NI NI A 802 O AHOH A 905 1555 1555 2.75 LINK NI NI A 802 O HOH A 959 1555 1555 2.53 CISPEP 1 ARG A 399 PRO A 400 0 -5.19 CISPEP 2 LYS A 438 PRO A 439 0 12.38 SITE 1 AC1 4 PRO A 520 TRP A 521 ARG A 695 HOH A 972 SITE 1 AC2 6 LEU A 404 ASP A 436 HOH A 905 HOH A 952 SITE 2 AC2 6 HOH A 959 HOH A 973 CRYST1 67.770 102.300 122.400 90.00 90.00 90.00 P 21 21 21 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 0.014756 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009775 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008170 0.00000