HEADER PROTEIN TRANSPORT 14-NOV-18 6I5R TITLE BLMNBP1 BINDING PROTEIN OF AN ABC TRANSPORTER FROM BIFIDOBACTERIUM TITLE 2 ANIMALIS SUBSP. LACTIS ATCC27673 IN COMPLEX WITH MANNOBIOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUGAR ABC TRANSPORTER SUBSTRATE-BINDING PROTEIN, BLMNBP1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BIFIDOBACTERIUM ANIMALIS SUBSP. LACTIS ATCC SOURCE 3 27673; SOURCE 4 ORGANISM_TAXID: 1167629; SOURCE 5 ATCC: ATCC27673; SOURCE 6 GENE: BLAC_00780; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PETM-11 KEYWDS SOLUTE BINDING PROTEIN, MANNOBIOSE, BIFIDOBACTERIUM ANIMALIS SUBSP. KEYWDS 2 LACTIS ATCC27673, BLAC_00780, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR M.ABOU HACHEM,M.EJBY,A.GUSKOV,D.J.SLOTBOOM REVDAT 4 15-MAY-24 6I5R 1 HETSYN LINK REVDAT 3 29-JUL-20 6I5R 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 17-JUL-19 6I5R 1 JRNL REVDAT 1 17-APR-19 6I5R 0 JRNL AUTH M.EJBY,A.GUSKOV,M.J.PICHLER,G.C.ZANTEN,E.SCHOOF,W.SABURI, JRNL AUTH 2 D.J.SLOTBOOM,M.ABOU HACHEM JRNL TITL TWO BINDING PROTEINS OF THE ABC TRANSPORTER THAT CONFERS JRNL TITL 2 GROWTH OF BIFIDOBACTERIUM ANIMALIS SUBSP. LACTIS ATCC27673 JRNL TITL 3 ON BETA-MANNAN POSSESS DISTINCT JRNL TITL 4 MANNO-OLIGOSACCHARIDE-BINDING PROFILES. JRNL REF MOL.MICROBIOL. V. 112 114 2019 JRNL REFN ESSN 1365-2958 JRNL PMID 30947380 JRNL DOI 10.1111/MMI.14257 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 56746 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2840 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 48.8543 - 4.3420 0.99 2869 154 0.2174 0.2544 REMARK 3 2 4.3420 - 3.4467 1.00 2760 141 0.1893 0.1961 REMARK 3 3 3.4467 - 3.0111 1.00 2733 150 0.1875 0.2188 REMARK 3 4 3.0111 - 2.7358 1.00 2742 142 0.2005 0.2373 REMARK 3 5 2.7358 - 2.5397 1.00 2697 137 0.2091 0.2423 REMARK 3 6 2.5397 - 2.3900 1.00 2693 149 0.2120 0.2705 REMARK 3 7 2.3900 - 2.2703 1.00 2697 132 0.2044 0.2034 REMARK 3 8 2.2703 - 2.1715 1.00 2703 150 0.2098 0.2369 REMARK 3 9 2.1715 - 2.0879 1.00 2682 147 0.2130 0.2242 REMARK 3 10 2.0879 - 2.0158 1.00 2666 135 0.2248 0.2674 REMARK 3 11 2.0158 - 1.9528 1.00 2701 137 0.2404 0.3007 REMARK 3 12 1.9528 - 1.8970 1.00 2654 145 0.2431 0.3085 REMARK 3 13 1.8970 - 1.8470 1.00 2672 139 0.2437 0.2853 REMARK 3 14 1.8470 - 1.8020 1.00 2664 142 0.2488 0.2578 REMARK 3 15 1.8020 - 1.7610 1.00 2672 140 0.2669 0.3181 REMARK 3 16 1.7610 - 1.7235 1.00 2668 141 0.2715 0.3187 REMARK 3 17 1.7235 - 1.6890 1.00 2640 138 0.2751 0.3036 REMARK 3 18 1.6890 - 1.6572 1.00 2672 141 0.2820 0.2795 REMARK 3 19 1.6572 - 1.6276 1.00 2651 139 0.3009 0.3274 REMARK 3 20 1.6276 - 1.6000 1.00 2670 141 0.3039 0.3388 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.420 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.44 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6I5R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1200012877. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99985 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 : 56799 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 48.832 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 11.80 REMARK 200 R MERGE (I) : 0.20440 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.5700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.80 REMARK 200 R MERGE FOR SHELL (I) : 2.07400 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: SAD REMARK 200 SOFTWARE USED: PHENIX 1.13_2998 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MOTHER LIQUOR: 0.1 M MES PH 5.5, 0.05 REMARK 280 M ZN-ACETATE AND 18% PEG 8000 PROTEIN CONC 15 MG/ML IN 10 MM MES REMARK 280 PH 6.5 AND 150 MM NACL + 1MM MANNOBIOSE DROPS SETUP 1 TO 1, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 278K 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 27.78000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.18500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.25000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.18500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.78000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.25000 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -307.0 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 GLY A 19 REMARK 465 ALA A 20 REMARK 465 ALA A 21 REMARK 465 CYS A 22 REMARK 465 GLY A 23 REMARK 465 GLY A 24 REMARK 465 ASP A 25 REMARK 465 ASP A 26 REMARK 465 LYS A 27 REMARK 465 GLY A 28 REMARK 465 GLY A 29 REMARK 465 ALA A 30 REMARK 465 LYS A 31 REMARK 465 THR A 32 REMARK 465 ALA A 33 REMARK 465 GLU A 34 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 HD2 HIS A 314 ZN ZN A 513 1.37 REMARK 500 ZN ZN A 511 O HOH A 601 1.56 REMARK 500 ZN ZN A 508 O HOH A 627 1.67 REMARK 500 ZN ZN A 512 O HOH A 850 1.68 REMARK 500 O HOH A 607 O HOH A 991 1.69 REMARK 500 O HOH A 1008 O HOH A 1069 1.72 REMARK 500 O HOH A 1005 O HOH A 1054 1.82 REMARK 500 O HOH A 982 O HOH A 987 1.83 REMARK 500 O HOH A 917 O HOH A 1042 1.83 REMARK 500 O HOH A 854 O HOH A 1003 1.84 REMARK 500 O HOH A 609 O HOH A 1000 1.84 REMARK 500 O HOH A 945 O HOH A 974 1.84 REMARK 500 OE2 GLU A 178 O HOH A 601 1.85 REMARK 500 O HOH A 966 O HOH A 1035 1.89 REMARK 500 O HOH A 724 O HOH A 1008 1.90 REMARK 500 OD2 ASP A 103 O HOH A 602 1.94 REMARK 500 O HOH A 963 O HOH A 977 1.94 REMARK 500 O HOH A 648 O HOH A 997 1.95 REMARK 500 O HOH A 921 O HOH A 943 1.95 REMARK 500 O HOH A 810 O HOH A 971 1.98 REMARK 500 OE1 GLU A 294 O HOH A 603 2.00 REMARK 500 O HOH A 1061 O HOH A 1096 2.01 REMARK 500 O HOH A 724 O HOH A 820 2.03 REMARK 500 OD2 ASP A 255 O HOH A 604 2.04 REMARK 500 O HOH A 624 O HOH A 1009 2.08 REMARK 500 O HOH A 1040 O HOH A 1073 2.08 REMARK 500 O GLY A 424 O HOH A 605 2.09 REMARK 500 O HOH A 689 O HOH A 856 2.09 REMARK 500 O HOH A 853 O HOH A 1071 2.09 REMARK 500 O HOH A 709 O HOH A 1027 2.10 REMARK 500 OE2 GLU A 191 O HOH A 606 2.10 REMARK 500 O HOH A 921 O HOH A 1035 2.12 REMARK 500 O HOH A 674 O HOH A 935 2.13 REMARK 500 O HOH A 614 O HOH A 813 2.14 REMARK 500 OD2 ASP A 416 O HOH A 607 2.14 REMARK 500 O HOH A 809 O HOH A 1006 2.15 REMARK 500 O HOH A 680 O HOH A 789 2.15 REMARK 500 OD1 ASP A 83 O HOH A 608 2.16 REMARK 500 OD2 ASP A 328 O HOH A 609 2.16 REMARK 500 OE2 GLU A 364 O HOH A 610 2.17 REMARK 500 O HOH A 605 O HOH A 888 2.17 REMARK 500 O HOH A 610 O HOH A 765 2.17 REMARK 500 O HOH A 627 O HOH A 901 2.18 REMARK 500 OD1 ASP A 460 O HOH A 611 2.18 REMARK 500 O HOH A 866 O HOH A 995 2.19 REMARK 500 OE1 GLU A 201 O HOH A 612 2.19 REMARK 500 O HOH A 722 O HOH A 865 2.19 REMARK 500 O HOH A 698 O HOH A 953 2.19 REMARK 500 O ASP A 150 O HOH A 613 2.19 REMARK 500 OE1 GLU A 459 O HOH A 614 2.19 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 O HOH A 606 O HOH A 836 2764 1.72 REMARK 500 O HOH A 624 O HOH A 713 3755 1.77 REMARK 500 O HOH A 918 O HOH A 1003 4466 1.81 REMARK 500 O HOH A 1007 O HOH A 1034 4556 1.82 REMARK 500 O HOH A 1021 O HOH A 1022 2665 1.89 REMARK 500 O HOH A 854 O HOH A 918 4566 1.90 REMARK 500 O HOH A 787 O HOH A 923 2665 1.93 REMARK 500 O HOH A 762 O HOH A 916 4566 2.02 REMARK 500 O HOH A 667 O HOH A 887 2665 2.10 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 254 C ASP A 255 N -0.208 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 ASP A 125 CB - CG - OD1 ANGL. DEV. = 7.4 DEGREES REMARK 500 ASP A 255 C - N - CA ANGL. DEV. = 15.6 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 PRO A 122 -157.18 -84.49 REMARK 500 TYR A 132 -33.09 -134.81 REMARK 500 LYS A 152 71.85 -113.48 REMARK 500 ASP A 155 39.67 38.72 REMARK 500 ALA A 226 -100.44 -106.46 REMARK 500 ALA A 253 66.47 -151.11 REMARK 500 HIS A 257 173.87 68.76 REMARK 500 HIS A 314 50.12 -117.67 REMARK 500 ASN A 423 47.50 -148.65 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 ZN A 516 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 103 OD2 REMARK 620 2 HOH A 602 O 55.5 REMARK 620 3 HOH A 671 O 84.7 71.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 510 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 125 OD1 REMARK 620 2 ASP A 125 OD2 56.8 REMARK 620 3 SER A 127 OG 63.0 91.0 REMARK 620 4 ASP A 408 OD1 64.6 105.9 99.5 REMARK 620 5 ASP A 408 OD2 119.5 162.4 102.3 60.8 REMARK 620 6 ASN A 412 OD1 118.6 83.1 170.5 89.2 85.1 REMARK 620 7 HOH A 635 O 168.7 115.3 111.4 126.7 70.6 65.1 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 508 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 138 OE1 REMARK 620 2 GLU A 138 OE2 58.0 REMARK 620 3 ASP A 448 OD2 37.9 86.2 REMARK 620 4 GLN A 452 NE2 40.2 86.3 3.3 REMARK 620 5 HOH A 901 O 95.4 84.0 126.4 129.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 506 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 155 OD1 REMARK 620 2 ASP A 155 OD2 56.7 REMARK 620 3 ASP A 431 OD1 88.0 95.9 REMARK 620 4 ASP A 435 OD1 87.9 98.1 2.7 REMARK 620 5 HOH A 876 O 112.3 90.2 33.5 35.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 511 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 178 OE1 REMARK 620 2 GLU A 178 OE2 62.6 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 509 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 195 OD1 REMARK 620 2 HOH A 640 O 92.5 REMARK 620 3 HOH A 845 O 90.1 102.1 REMARK 620 4 HOH A 982 O 99.4 111.6 144.3 REMARK 620 5 HOH A 987 O 96.3 162.9 92.6 52.4 REMARK 620 6 HOH A1068 O 161.2 78.5 75.9 99.2 96.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 512 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 214 OE1 REMARK 620 2 HOH A 764 O 92.7 REMARK 620 3 HOH A 838 O 91.9 154.0 REMARK 620 4 HOH A1051 O 151.2 72.3 91.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 507 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 215 OD1 REMARK 620 2 GLU A 462 O 55.7 REMARK 620 3 GLU A 462 OXT 52.6 3.4 REMARK 620 4 HOH A 666 O 89.4 130.6 127.7 REMARK 620 5 HOH A 819 O 91.3 54.3 54.8 99.0 REMARK 620 6 HOH A 830 O 91.0 122.1 122.0 88.1 172.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 504 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 257 NE2 REMARK 620 2 HOH A 697 O 92.3 REMARK 620 3 HOH A 724 O 82.6 120.6 REMARK 620 4 HOH A 798 O 95.6 110.5 129.0 REMARK 620 5 HOH A1008 O 129.0 80.1 60.2 134.5 REMARK 620 6 HOH A1069 O 177.7 87.9 95.3 86.4 48.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 313 OD2 REMARK 620 2 ASP A 365 OD1 52.5 REMARK 620 3 HOH A 653 O 82.2 110.1 REMARK 620 4 HOH A 655 O 89.0 43.5 96.8 REMARK 620 5 HOH A 911 O 85.7 61.7 168.0 82.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 513 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 317 OD2 REMARK 620 2 HOH A 689 O 94.8 REMARK 620 3 HOH A1031 O 99.4 59.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 505 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 404 OE2 REMARK 620 2 GLU A 449 OE1 98.4 REMARK 620 3 GLU A 449 OE2 97.2 3.7 REMARK 620 4 HOH A 918 O 100.9 7.9 5.4 REMARK 620 5 HOH A 978 O 101.8 4.7 4.6 4.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 514 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 462 OE1 REMARK 620 2 HOH A 956 O 117.0 REMARK 620 3 HOH A1028 O 152.3 89.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 515 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 780 O REMARK 620 2 HOH A 788 O 67.7 REMARK 620 3 HOH A 868 O 100.8 100.9 REMARK 620 N 1 2 DBREF 6I5R A 19 462 PDB 6I5R 6I5R 19 462 SEQRES 1 A 444 GLY ALA ALA CYS GLY GLY ASP ASP LYS GLY GLY ALA LYS SEQRES 2 A 444 THR ALA GLU GLY ASN LYS THR GLY ILE THR TYR PRO GLU SEQRES 3 A 444 ILE LYS LEU GLY GLU THR GLY LYS ASP ILE LYS THR THR SEQRES 4 A 444 ILE THR PHE MET ASN ASN ARG THR ASP MET ASN LEU ASP SEQRES 5 A 444 THR TYR PRO GLY LYS ASN TRP LYS SER TYR ILE GLU ASP SEQRES 6 A 444 PHE ASN LYS MET TYR PRO ASN ILE THR VAL LYS VAL GLN SEQRES 7 A 444 THR ASP SER ASN TYR ALA ASP SER ALA LEU THR ARG LEU SEQRES 8 A 444 GLN ALA ASN ASN ASP SER TRP ASP ILE MET MET ILE PRO SEQRES 9 A 444 ALA VAL ASP LYS SER GLU PHE SER ASN TYR PHE VAL PRO SEQRES 10 A 444 TYR GLY GLU THR SER GLU MET GLU LYS VAL ILE LYS LEU SEQRES 11 A 444 ALA ASP GLU LYS ALA TYR ASP GLY GLN THR TYR GLY ILE SEQRES 12 A 444 ALA ASN ASN GLY VAL THR ALA GLY ILE VAL TYR ASN LYS SEQRES 13 A 444 LYS VAL PHE GLU GLU ALA GLY ILE LYS GLU LEU PRO LYS SEQRES 14 A 444 THR PRO GLU GLU PHE GLN ALA ASP LEU LYS LEU ILE LYS SEQRES 15 A 444 GLU LYS THR LYS ALA VAL PRO LEU TYR THR ASN PHE VAL SEQRES 16 A 444 GLU ASP TRP ALA MET GLY ALA TRP ASP GLN TYR ILE ALA SEQRES 17 A 444 GLY ASN ALA THR GLY ASP PRO LYS PHE MET ASN GLN VAL SEQRES 18 A 444 LEU PRO THR THR LYS GLU PRO PHE LYS LYS ASP ALA SER SEQRES 19 A 444 ALA PRO ASP THR HIS PRO TYR ALA VAL TYR LYS THR LEU SEQRES 20 A 444 TYR ASP ALA VAL ALA ASN GLY TYR THR GLU GLU ASP TYR SEQRES 21 A 444 SER THR THR ASP TRP GLU SER SER LYS GLY LYS MET ASN SEQRES 22 A 444 ASN GLY GLU ILE ALA THR MET VAL LEU GLY ALA TRP ALA SEQRES 23 A 444 VAL PRO GLN MET LYS GLN ALA GLY ASP HIS PRO ASP ASP SEQRES 24 A 444 ILE GLY TYR MET PRO PHE PRO ILE THR VAL ASP GLY LYS SEQRES 25 A 444 GLN TYR ALA THR ILE ALA GLY ASP TYR SER TYR GLY ILE SEQRES 26 A 444 ASN LYS ASN ILE SER LYS GLU LYS GLN GLU ALA SER MET SEQRES 27 A 444 ILE PHE VAL LYS TRP MET THR GLU ASP SER GLY PHE ALA SEQRES 28 A 444 LYS ASN GLU GLY GLY ILE PRO ILE LYS ALA ASP ASP GLU SEQRES 29 A 444 SER MET PRO GLU THR TYR GLU THR PHE SER ASP VAL GLU SEQRES 30 A 444 LEU ILE THR ASP ALA PRO ALA LYS GLU GLY GLN GLU ASP SEQRES 31 A 444 LEU LEU ALA ASN VAL ASN SER ASP SER GLU LEU GLY ILE SEQRES 32 A 444 ASN ASN GLY ASN GLY LYS LYS ILE GLN ASP ILE VAL VAL SEQRES 33 A 444 ASP ALA ALA ASN ARG THR ARG THR ILE ASP GLN ILE MET SEQRES 34 A 444 ASP GLU TRP ASN GLN LYS TRP ALA LYS ALA VAL GLU ASP SEQRES 35 A 444 ASN GLU HET BMA B 1 23 HET BMA B 2 22 HET ZN A 503 1 HET ZN A 504 1 HET ZN A 505 1 HET ZN A 506 1 HET ZN A 507 1 HET ZN A 508 1 HET ZN A 509 1 HET ZN A 510 1 HET ZN A 511 1 HET ZN A 512 1 HET ZN A 513 1 HET ZN A 514 1 HET ZN A 515 1 HET ZN A 516 1 HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM ZN ZINC ION HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 2 BMA 2(C6 H12 O6) FORMUL 3 ZN 14(ZN 2+) FORMUL 17 HOH *496(H2 O) HELIX 1 AA1 THR A 41 ILE A 45 5 5 HELIX 2 AA2 THR A 65 LEU A 69 5 5 HELIX 3 AA3 ASN A 76 TYR A 88 1 13 HELIX 4 AA4 ASN A 100 ASN A 112 1 13 HELIX 5 AA5 ASP A 125 TYR A 132 5 8 HELIX 6 AA6 THR A 139 GLU A 143 1 5 HELIX 7 AA7 LYS A 174 GLY A 181 1 8 HELIX 8 AA8 THR A 188 THR A 203 1 16 HELIX 9 AA9 GLU A 214 ALA A 220 1 7 HELIX 10 AB1 TRP A 221 ILE A 225 5 5 HELIX 11 AB2 ALA A 226 GLY A 231 1 6 HELIX 12 AB3 GLN A 238 THR A 243 1 6 HELIX 13 AB4 THR A 256 ASN A 271 1 16 HELIX 14 AB5 ASP A 277 THR A 281 5 5 HELIX 15 AB6 ASP A 282 ASN A 292 1 11 HELIX 16 AB7 TRP A 303 GLN A 310 1 8 HELIX 17 AB8 HIS A 314 ASP A 316 5 3 HELIX 18 AB9 SER A 348 ASP A 365 1 18 HELIX 19 AC1 GLY A 367 GLU A 372 1 6 HELIX 20 AC2 ASP A 408 GLU A 418 1 11 HELIX 21 AC3 GLY A 426 ARG A 439 1 14 HELIX 22 AC4 THR A 442 GLU A 462 1 21 SHEET 1 AA1 5 ILE A 91 THR A 97 0 SHEET 2 AA1 5 THR A 56 ASN A 62 1 N ILE A 58 O LYS A 94 SHEET 3 AA1 5 ILE A 118 MET A 120 1 O ILE A 118 N MET A 61 SHEET 4 AA1 5 SER A 340 ILE A 343 -1 O GLY A 342 N MET A 119 SHEET 5 AA1 5 ILE A 161 ALA A 162 -1 N ILE A 161 O TYR A 341 SHEET 1 AA2 3 GLY A 137 GLU A 138 0 SHEET 2 AA2 3 GLN A 157 THR A 158 -1 O THR A 158 N GLY A 137 SHEET 3 AA2 3 ALA A 153 TYR A 154 -1 N TYR A 154 O GLN A 157 SHEET 1 AA3 4 VAL A 206 LEU A 208 0 SHEET 2 AA3 4 ILE A 295 GLY A 301 1 O ALA A 296 N VAL A 206 SHEET 3 AA3 4 GLY A 165 ASN A 173 -1 N VAL A 171 O MET A 298 SHEET 4 AA3 4 ILE A 318 PRO A 322 -1 O GLY A 319 N TYR A 172 SHEET 1 AA4 5 VAL A 206 LEU A 208 0 SHEET 2 AA4 5 ILE A 295 GLY A 301 1 O ALA A 296 N VAL A 206 SHEET 3 AA4 5 GLY A 165 ASN A 173 -1 N VAL A 171 O MET A 298 SHEET 4 AA4 5 TYR A 332 GLY A 337 -1 O ALA A 336 N VAL A 166 SHEET 5 AA4 5 GLU A 395 ILE A 397 1 O ILE A 397 N ILE A 335 LINK O4 BMA B 1 C1 BMA B 2 1555 1555 1.40 LINK OD2 ASP A 103 ZN ZN A 516 1555 1555 2.08 LINK OD1 ASP A 125 ZN ZN A 510 1555 1555 2.34 LINK OD2 ASP A 125 ZN ZN A 510 1555 1555 2.09 LINK OG SER A 127 ZN ZN A 510 1555 1555 2.34 LINK OE1 GLU A 138 ZN ZN A 508 1555 1555 2.09 LINK OE2 GLU A 138 ZN ZN A 508 1555 1555 2.29 LINK OD1 ASP A 155 ZN ZN A 506 1555 1555 2.03 LINK OD2 ASP A 155 ZN ZN A 506 1555 1555 2.38 LINK OE1 GLU A 178 ZN ZN A 511 1555 1555 1.90 LINK OE2 GLU A 178 ZN ZN A 511 1555 1555 2.21 LINK OD1 ASP A 195 ZN ZN A 509 1555 1555 2.18 LINK OE1 GLU A 214 ZN ZN A 512 1555 1555 2.22 LINK OD1 ASP A 215 ZN ZN A 507 1555 1555 2.14 LINK NE2 HIS A 257 ZN ZN A 504 1555 1555 1.99 LINK OD2 ASP A 313 ZN ZN A 503 1555 1555 1.94 LINK OD2 ASP A 317 ZN ZN A 513 1555 1555 2.11 LINK OD1 ASP A 365 ZN ZN A 503 1555 4556 2.05 LINK OE2 GLU A 404 ZN ZN A 505 1555 4566 2.17 LINK OD1 ASP A 408 ZN ZN A 510 1555 1555 2.20 LINK OD2 ASP A 408 ZN ZN A 510 1555 1555 2.11 LINK OD1 ASN A 412 ZN ZN A 510 1555 1555 2.28 LINK OD1 ASP A 431 ZN ZN A 506 1555 4466 2.03 LINK OD1 ASP A 435 ZN ZN A 506 1555 4466 1.97 LINK OD2 ASP A 448 ZN ZN A 508 1555 4466 1.96 LINK OE1 GLU A 449 ZN ZN A 505 1555 1555 2.65 LINK OE2 GLU A 449 ZN ZN A 505 1555 1555 1.98 LINK NE2 GLN A 452 ZN ZN A 508 1555 4466 2.38 LINK O GLU A 462 ZN ZN A 507 1555 4566 2.34 LINK OXT GLU A 462 ZN ZN A 507 1555 4566 2.10 LINK OE1 GLU A 462 ZN ZN A 514 1555 1555 2.15 LINK ZN ZN A 503 O HOH A 653 1555 4456 2.37 LINK ZN ZN A 503 O HOH A 655 1555 4456 1.85 LINK ZN ZN A 503 O HOH A 911 1555 1555 2.37 LINK ZN ZN A 504 O HOH A 697 1555 1555 2.24 LINK ZN ZN A 504 O HOH A 724 1555 1555 2.02 LINK ZN ZN A 504 O HOH A 798 1555 1555 1.76 LINK ZN ZN A 504 O HOH A1008 1555 1555 1.74 LINK ZN ZN A 504 O HOH A1069 1555 1555 2.26 LINK ZN ZN A 505 O HOH A 918 1555 1555 2.09 LINK ZN ZN A 505 O HOH A 978 1555 4466 1.91 LINK ZN ZN A 506 O HOH A 876 1555 4566 1.89 LINK ZN ZN A 507 O HOH A 666 1555 1555 2.06 LINK ZN ZN A 507 O HOH A 819 1555 1555 2.10 LINK ZN ZN A 507 O HOH A 830 1555 4466 2.04 LINK ZN ZN A 508 O HOH A 901 1555 1555 2.10 LINK ZN ZN A 509 O HOH A 640 1555 1555 2.37 LINK ZN ZN A 509 O HOH A 845 1555 1555 2.08 LINK ZN ZN A 509 O HOH A 982 1555 1555 2.01 LINK ZN ZN A 509 O HOH A 987 1555 1555 2.13 LINK ZN ZN A 509 O HOH A1068 1555 1555 2.06 LINK ZN ZN A 510 O HOH A 635 1555 1555 2.13 LINK ZN ZN A 512 O HOH A 764 1555 1555 2.52 LINK ZN ZN A 512 O HOH A 838 1555 1555 1.80 LINK ZN ZN A 512 O HOH A1051 1555 1555 2.02 LINK ZN ZN A 513 O HOH A 689 1555 1555 2.13 LINK ZN ZN A 513 O HOH A1031 1555 1555 2.64 LINK ZN ZN A 514 O HOH A 956 1555 1555 2.59 LINK ZN ZN A 514 O HOH A1028 1555 1555 1.96 LINK ZN ZN A 515 O HOH A 780 1555 1555 2.64 LINK ZN ZN A 515 O HOH A 788 1555 1555 2.05 LINK ZN ZN A 515 O HOH A 868 1555 1555 1.80 LINK ZN ZN A 516 O HOH A 602 1555 1555 2.08 LINK ZN ZN A 516 O HOH A 671 1555 1555 1.85 CRYST1 55.560 74.500 102.370 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 0.017999 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013423 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009768 0.00000