PDB Short entry for 5VC1 HEADER CELL ADHESION 30-MAR-17 5VC1 TITLE CRYSTAL STRUCTURE OF L-SELECTIN LECTIN/EGF DOMAINS CAVEAT 5VC1 MAN B 3 HAS WRONG CHIRALITY AT ATOM C1 BMA B 4 HAS WRONG CAVEAT 2 5VC1 CHIRALITY AT ATOM C1 BMA B 5 HAS WRONG CHIRALITY AT ATOM C1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: L-SELECTIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 39-195; COMPND 5 SYNONYM: CD62 ANTIGEN-LIKE FAMILY MEMBER L,LEUKOCYTE ADHESION COMPND 6 MOLECULE 1,LAM-1,LEUKOCYTE SURFACE ANTIGEN LEU-8,LEUKOCYTE- COMPND 7 ENDOTHELIAL CELL ADHESION MOLECULE 1,LECAM1,LYMPH NODE HOMING COMPND 8 RECEPTOR,TQ1,GP90-MEL; COMPND 9 ENGINEERED: YES; COMPND 10 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: SELL, LNHR, LYAM1; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: HEK293F KEYWDS L-SELECTIN; GLYCOPROTEIN, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR S.WEDEPOHL,J.DERNEDDE,A.VAHEDI-FARIDI,R.TAUBER,W.SAENGER,H.BULUT REVDAT 5 17-JAN-24 5VC1 1 HETSYN LINK REVDAT 4 29-JUL-20 5VC1 1 CAVEAT COMPND REMARK HETNAM REVDAT 4 2 1 LINK SITE ATOM REVDAT 3 16-OCT-19 5VC1 1 REMARK REVDAT 2 12-JUL-17 5VC1 1 REVDAT 1 14-JUN-17 5VC1 0 JRNL AUTH S.WEDEPOHL,J.DERNEDDE,A.VAHEDI-FARIDI,R.TAUBER,W.SAENGER, JRNL AUTH 2 H.BULUT JRNL TITL REDUCING MACRO- AND MICROHETEROGENEITY OF N-GLYCANS ENABLES JRNL TITL 2 THE CRYSTAL STRUCTURE OF THE LECTIN AND EGF-LIKE DOMAINS OF JRNL TITL 3 HUMAN L-SELECTIN TO BE SOLVED AT 1.9 ANGSTROM RESOLUTION. JRNL REF CHEMBIOCHEM V. 18 1338 2017 JRNL REFN ESSN 1439-7633 JRNL PMID 28489325 JRNL DOI 10.1002/CBIC.201700220 REMARK 2 REMARK 2 RESOLUTION. 1.94 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) 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) : 1.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.030 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 20673 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1034 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 31.7009 - 3.7100 1.00 2878 152 0.1808 0.2086 REMARK 3 2 3.7100 - 2.9454 1.00 2821 148 0.2016 0.2206 REMARK 3 3 2.9454 - 2.5733 1.00 2800 148 0.2185 0.2632 REMARK 3 4 2.5733 - 2.3381 1.00 2780 146 0.2108 0.2419 REMARK 3 5 2.3381 - 2.1705 1.00 2793 147 0.2162 0.2451 REMARK 3 6 2.1705 - 2.0426 1.00 2780 146 0.2221 0.2688 REMARK 3 7 2.0426 - 1.9403 1.00 2787 147 0.2178 0.2290 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.870 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 1403 REMARK 3 ANGLE : 0.900 1881 REMARK 3 CHIRALITY : 0.053 192 REMARK 3 PLANARITY : 0.005 230 REMARK 3 DIHEDRAL : 9.192 1112 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 5VC1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1000227192. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-FEB-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20674 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.940 REMARK 200 RESOLUTION RANGE LOW (A) : 31.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.8200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: PHENIX REMARK 200 STARTING MODEL: 3CFW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM CACODYLATE PH 7.5, 200 REMARK 280 MM CALCIUM ACETATE, 40% (V/V) PEG 600, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 Z,X,Y REMARK 290 6555 Z,-X,-Y REMARK 290 7555 -Z,-X,Y REMARK 290 8555 -Z,X,-Y REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z,-X REMARK 290 11555 Y,-Z,-X REMARK 290 12555 -Y,-Z,X REMARK 290 13555 X+1/2,Y+1/2,Z+1/2 REMARK 290 14555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 15555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 16555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 17555 Z+1/2,X+1/2,Y+1/2 REMARK 290 18555 Z+1/2,-X+1/2,-Y+1/2 REMARK 290 19555 -Z+1/2,-X+1/2,Y+1/2 REMARK 290 20555 -Z+1/2,X+1/2,-Y+1/2 REMARK 290 21555 Y+1/2,Z+1/2,X+1/2 REMARK 290 22555 -Y+1/2,Z+1/2,-X+1/2 REMARK 290 23555 Y+1/2,-Z+1/2,-X+1/2 REMARK 290 24555 -Y+1/2,-Z+1/2,X+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 0.00000 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 0.00000 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 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 59.29900 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 59.29900 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 59.29900 REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 59.29900 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 59.29900 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 59.29900 REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 59.29900 REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 59.29900 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 59.29900 REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 59.29900 REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 59.29900 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 59.29900 REMARK 290 SMTRY1 17 0.000000 0.000000 1.000000 59.29900 REMARK 290 SMTRY2 17 1.000000 0.000000 0.000000 59.29900 REMARK 290 SMTRY3 17 0.000000 1.000000 0.000000 59.29900 REMARK 290 SMTRY1 18 0.000000 0.000000 1.000000 59.29900 REMARK 290 SMTRY2 18 -1.000000 0.000000 0.000000 59.29900 REMARK 290 SMTRY3 18 0.000000 -1.000000 0.000000 59.29900 REMARK 290 SMTRY1 19 0.000000 0.000000 -1.000000 59.29900 REMARK 290 SMTRY2 19 -1.000000 0.000000 0.000000 59.29900 REMARK 290 SMTRY3 19 0.000000 1.000000 0.000000 59.29900 REMARK 290 SMTRY1 20 0.000000 0.000000 -1.000000 59.29900 REMARK 290 SMTRY2 20 1.000000 0.000000 0.000000 59.29900 REMARK 290 SMTRY3 20 0.000000 -1.000000 0.000000 59.29900 REMARK 290 SMTRY1 21 0.000000 1.000000 0.000000 59.29900 REMARK 290 SMTRY2 21 0.000000 0.000000 1.000000 59.29900 REMARK 290 SMTRY3 21 1.000000 0.000000 0.000000 59.29900 REMARK 290 SMTRY1 22 0.000000 -1.000000 0.000000 59.29900 REMARK 290 SMTRY2 22 0.000000 0.000000 1.000000 59.29900 REMARK 290 SMTRY3 22 -1.000000 0.000000 0.000000 59.29900 REMARK 290 SMTRY1 23 0.000000 1.000000 0.000000 59.29900 REMARK 290 SMTRY2 23 0.000000 0.000000 -1.000000 59.29900 REMARK 290 SMTRY3 23 -1.000000 0.000000 0.000000 59.29900 REMARK 290 SMTRY1 24 0.000000 -1.000000 0.000000 59.29900 REMARK 290 SMTRY2 24 0.000000 0.000000 -1.000000 59.29900 REMARK 290 SMTRY3 24 1.000000 0.000000 0.000000 59.29900 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: 1610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 13.0 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 GLN A 154 REMARK 465 PHE A 155 REMARK 465 VAL A 156 REMARK 465 ILE A 157 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 SG CYS A 127 SG CYS A 142 1.30 REMARK 500 CB CYS A 127 SG CYS A 142 2.17 REMARK 500 SG CYS A 127 CB CYS A 142 2.19 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 CYS A 127 CB - CA - C ANGL. DEV. = 8.9 DEGREES REMARK 500 CYS A 127 N - CA - C ANGL. DEV. = -25.3 DEGREES REMARK 500 SER A 128 N - CA - C ANGL. DEV. = 18.3 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 TYR A 23 -141.51 -131.96 REMARK 500 TYR A 48 -157.03 63.84 REMARK 500 ASN A 75 41.57 -144.02 REMARK 500 TRP A 125 -0.34 114.47 REMARK 500 SER A 128 58.67 -65.88 REMARK 500 GLN A 139 -157.07 -162.98 REMARK 500 ASP A 145 -130.98 -79.02 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 CA A 209 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 80 OE1 REMARK 620 2 ASN A 82 OD1 74.7 REMARK 620 3 GLU A 88 OE1 143.5 71.8 REMARK 620 4 ASN A 105 OD1 69.6 141.8 146.0 REMARK 620 5 ASP A 106 O 129.0 140.9 74.3 75.3 REMARK 620 6 ASP A 106 OD1 71.7 83.7 90.5 97.6 77.8 REMARK 620 7 BMA B 4 O3 81.8 87.9 83.0 100.0 69.0 10.3 REMARK 620 8 BMA B 4 O4 80.2 90.4 85.9 96.7 68.3 9.7 3.4 REMARK 620 N 1 2 3 4 5 6 7 DBREF 5VC1 A 1 157 UNP P14151 LYAM1_HUMAN 39 195 SEQADV 5VC1 GLN A 22 UNP P14151 ASN 60 ENGINEERED MUTATION SEQADV 5VC1 GLN A 139 UNP P14151 ASN 177 ENGINEERED MUTATION SEQRES 1 A 157 TRP THR TYR HIS TYR SER GLU LYS PRO MET ASN TRP GLN SEQRES 2 A 157 ARG ALA ARG ARG PHE CYS ARG ASP GLN TYR THR ASP LEU SEQRES 3 A 157 VAL ALA ILE GLN ASN LYS ALA GLU ILE GLU TYR LEU GLU SEQRES 4 A 157 LYS THR LEU PRO PHE SER ARG SER TYR TYR TRP ILE GLY SEQRES 5 A 157 ILE ARG LYS ILE GLY GLY ILE TRP THR TRP VAL GLY THR SEQRES 6 A 157 ASN LYS SER LEU THR GLU GLU ALA GLU ASN TRP GLY ASP SEQRES 7 A 157 GLY GLU PRO ASN ASN LYS LYS ASN LYS GLU ASP CYS VAL SEQRES 8 A 157 GLU ILE TYR ILE LYS ARG ASN LYS ASP ALA GLY LYS TRP SEQRES 9 A 157 ASN ASP ASP ALA CYS HIS LYS LEU LYS ALA ALA LEU CYS SEQRES 10 A 157 TYR THR ALA SER CYS GLN PRO TRP SER CYS SER GLY HIS SEQRES 11 A 157 GLY GLU CYS VAL GLU ILE ILE ASN GLN TYR THR CYS ASN SEQRES 12 A 157 CYS ASP VAL GLY TYR TYR GLY PRO GLN CYS GLN PHE VAL SEQRES 13 A 157 ILE HET NAG B 1 14 HET NAG B 2 14 HET MAN B 3 11 HET BMA B 4 11 HET BMA B 5 11 HET PG4 A 206 13 HET PEG A 207 7 HET GOL A 208 6 HET CA A 209 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM PG4 TETRAETHYLENE GLYCOL HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM GOL GLYCEROL HETNAM CA CALCIUM ION 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 MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 NAG 2(C8 H15 N O6) FORMUL 2 MAN C6 H12 O6 FORMUL 2 BMA 2(C6 H12 O6) FORMUL 3 PG4 C8 H18 O5 FORMUL 4 PEG C4 H10 O3 FORMUL 5 GOL C3 H8 O3 FORMUL 6 CA CA 2+ FORMUL 7 HOH *77(H2 O) HELIX 1 AA1 ASN A 11 TYR A 23 1 13 HELIX 2 AA2 ASN A 31 LEU A 42 1 12 HELIX 3 AA3 ASN A 83 LYS A 87 5 5 SHEET 1 AA1 3 THR A 2 TYR A 5 0 SHEET 2 AA1 3 ALA A 114 THR A 119 -1 O CYS A 117 N HIS A 4 SHEET 3 AA1 3 ASP A 25 LEU A 26 -1 N ASP A 25 O TYR A 118 SHEET 1 AA2 5 THR A 2 TYR A 5 0 SHEET 2 AA2 5 ALA A 114 THR A 119 -1 O CYS A 117 N HIS A 4 SHEET 3 AA2 5 TYR A 49 TRP A 50 1 N TRP A 50 O ALA A 114 SHEET 4 AA2 5 CYS A 90 ILE A 93 -1 O ILE A 93 N TYR A 49 SHEET 5 AA2 5 TRP A 104 ASP A 107 -1 O ASP A 107 N CYS A 90 SHEET 1 AA3 3 ILE A 53 ILE A 56 0 SHEET 2 AA3 3 ILE A 59 TRP A 62 -1 O THR A 61 N ARG A 54 SHEET 3 AA3 3 LYS A 67 SER A 68 -1 O LYS A 67 N TRP A 62 SHEET 1 AA4 2 GLU A 132 ILE A 136 0 SHEET 2 AA4 2 GLN A 139 ASN A 143 -1 O THR A 141 N VAL A 134 SSBOND 1 CYS A 19 CYS A 117 1555 1555 2.06 SSBOND 2 CYS A 90 CYS A 109 1555 1555 2.04 SSBOND 3 CYS A 122 CYS A 133 1555 1555 2.04 SSBOND 4 CYS A 144 CYS A 153 1555 1555 2.03 LINK ND2 ASN A 66 C1 NAG B 1 1555 1555 1.42 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.40 LINK O4 NAG B 2 C1 MAN B 3 1555 1555 1.41 LINK O3 MAN B 3 C1 BMA B 4 1555 1555 1.45 LINK O6 MAN B 3 C1 BMA B 5 1555 1555 1.44 LINK OE1 GLU A 80 CA CA A 209 1555 1555 2.48 LINK OD1 ASN A 82 CA CA A 209 1555 1555 2.47 LINK OE1 GLU A 88 CA CA A 209 1555 1555 2.38 LINK OD1 ASN A 105 CA CA A 209 1555 1555 2.39 LINK O ASP A 106 CA CA A 209 1555 1555 2.48 LINK OD1 ASP A 106 CA CA A 209 1555 1555 2.38 LINK CA CA A 209 O3 BMA B 4 24555 1555 2.49 LINK CA CA A 209 O4 BMA B 4 24555 1555 2.60 CISPEP 1 GLU A 80 PRO A 81 0 -2.43 CRYST1 118.598 118.598 118.598 90.00 90.00 90.00 I 2 3 24 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 0.008432 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008432 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008432 0.00000