HEADER CELL ADHESION PROTEIN 08-JAN-02 1GSM TITLE A REASSESSMENT OF THE MADCAM-1 STRUCTURE AND ITS ROLE IN INTEGRIN TITLE 2 RECOGNITION. COMPND MOL_ID: 1; COMPND 2 MOLECULE: MUCOSAL ADDRESSIN CELL ADHESION MOLECULE-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: EXTRACELLULAR REGION WITH TWO IG-LIKE DOMAINS; COMPND 5 SYNONYM: MADCAM-1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 CELL: HEMATOPOIETIC AND ENDOTHELIAL CELLS; SOURCE 6 EXPRESSION_SYSTEM: MUS MUSCULUS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 10090; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: NSO CELLS KEYWDS CELL ADHESION PROTEIN, MADCAM-1, IMMUNOGLOBULIN FOLD, I-SET FOLD, KEYWDS 2 CELL ADHESION GLYCOPROTEIN, INTEGRIN RECOGINITION, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.DANDO,K.W.WILKINSON,S.ORTLEPP,D.J.KING,R.L.BRADY REVDAT 7 23-OCT-24 1GSM 1 REMARK REVDAT 6 13-DEC-23 1GSM 1 REMARK REVDAT 5 24-JUL-19 1GSM 1 REMARK REVDAT 4 24-FEB-09 1GSM 1 VERSN REVDAT 3 05-JUL-05 1GSM 1 SOURCE REVDAT 2 05-MAY-05 1GSM 1 JRNL REVDAT 1 29-JAN-02 1GSM 0 JRNL AUTH J.DANDO,K.W.WILKINSON,S.ORTLEPP,D.J.KING,R.L.BRADY JRNL TITL A REASSESSMENT OF THE MADCAM-1 STRUCTURE AND ITS ROLE IN JRNL TITL 2 INTEGRIN RECOGNITION JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 58 233 2002 JRNL REFN ISSN 0907-4449 JRNL PMID 11807247 JRNL DOI 10.1107/S0907444901020522 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.0 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.49 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 16764 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) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 901 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1185 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2240 REMARK 3 BIN FREE R VALUE SET COUNT : 54 REMARK 3 BIN FREE R VALUE : 0.3000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1531 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 184 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.167 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.151 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.113 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.747 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.943 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1452 ; 0.014 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; NULL ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): 1988 ; 1.858 ; 1.982 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 236 ; 0.116 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1106 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 563 ; 0.225 ; 0.300 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): 228 ; 0.182 ; 0.500 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): 54 ; 0.224 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 36 ; 0.307 ; 0.500 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): 970 ; 1.063 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1559 ; 1.935 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 482 ; 2.885 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 429 ; 4.763 ; 4.500 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 : NULL 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 : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ATOMS WHICH WERE NOT VISIBLE IN THE REMARK 3 ELECTRON DENSITY MAPS HAVE BEEN GIVEN ZERO OCCUPANCY IN THIS PDB REMARK 3 FILE. REMARK 4 REMARK 4 1GSM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-JAN-02. REMARK 100 THE DEPOSITION ID IS D_1290009218. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 102574 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.03300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 43.3000 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 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: CCP4 REMARK 200 STARTING MODEL: PDB ENTRY 1BQS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN SOLUTION:10 MG/ML. REMARK 280 CRYSTALLIZATION SOLUTION: 16% PEG 4000, 0.5M LI2SO4, PH 7.75., REMARK 280 PH 8.00 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.25000 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 35.25000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 32.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.60000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 32.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.60000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 35.25000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 32.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 49.60000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 35.25000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 32.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 49.60000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 400 REMARK 400 COMPOUND REMARK 400 MUCOSAL ADDRESSIN CELL ADHESION MOLECULE-1 (MADCAM-1) IS REMARK 400 IMPORTANT IN LYMPHOCYTE HOMING TO MUCOSAL TISSUES. HUMAN REMARK 400 MADCAM-1 CONTAINS TWO IG-LIKE DOMAINS, A MUCIN-LIKE REGION, REMARK 400 A TRANSMEMBRANE DOMAIN AND A CYTOPLASMIC DOMAIN. IT HAS A REMARK 400 UNIQUE DUAL FUNCTION AMONG ADHESION MOLECULES. IT BINDS THE REMARK 400 INTEGRIN ALPHA4BETA7IG-LIKE DOMAINS, AND WHEN APPROPRIATE, REMARK 400 O-GLYCOSYLATED MOLECULES BIND THROUGH ITS MUCIN-LIKE REMARK 400 REGION. 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 -3 REMARK 465 SER A -2 REMARK 465 LEU A -1 REMARK 465 GLN A 0 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 THR A 43 REMARK 475 SER A 44 REMARK 475 GLU A 150 REMARK 475 GLU A 151 REMARK 475 GLU A 152 REMARK 475 PRO A 153 REMARK 475 GLN A 154 REMARK 475 GLY A 155 REMARK 475 ASP A 156 REMARK 475 GLU A 157 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 2 CD CE NZ REMARK 480 ARG A 32 CG CD NE CZ NH1 NH2 REMARK 480 LEU A 45 CB CG CD1 CD2 REMARK 480 ASP A 158 N CA C O REMARK 480 ILE A 203 CG1 CG2 CD1 REMARK 480 GLU A 204 CB CG CD OE1 OE2 REMARK 480 ARG A 206 CB CG CD NE CZ NH1 NH2 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 NE2 GLN A 147 OE2 GLU A 150 1.37 REMARK 500 CG GLU A 150 O HOH A 2145 1.51 REMARK 500 CB GLU A 150 O HOH A 2145 1.58 REMARK 500 CD GLU A 150 O HOH A 2145 1.81 REMARK 500 OE1 GLU A 150 O HOH A 2145 1.96 REMARK 500 OG1 THR A 69 NE2 GLN A 86 2.11 REMARK 500 NZ LYS A 2 O HOH A 2004 2.18 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 CG2 THR A 43 O ARG A 60 4566 1.12 REMARK 500 CG2 THR A 43 C ARG A 60 4566 2.12 REMARK 500 CB THR A 43 O ARG A 60 4566 2.17 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 ARG A 32 CB ARG A 32 CG -0.494 REMARK 500 ASP A 42 C THR A 43 N -0.372 REMARK 500 LEU A 45 CA LEU A 45 CB -0.395 REMARK 500 ASP A 158 CA ASP A 158 CB 0.219 REMARK 500 ILE A 203 CB ILE A 203 CG1 0.284 REMARK 500 GLU A 204 CA GLU A 204 CB -0.312 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 LYS A 2 CG - CD - CE ANGL. DEV. = 22.4 DEGREES REMARK 500 ASP A 42 CA - C - N ANGL. DEV. = -41.9 DEGREES REMARK 500 ASP A 42 O - C - N ANGL. DEV. = -14.8 DEGREES REMARK 500 THR A 43 C - N - CA ANGL. DEV. = -39.9 DEGREES REMARK 500 ASP A 107 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 GLU A 149 CA - C - N ANGL. DEV. = -34.1 DEGREES REMARK 500 GLU A 149 O - C - N ANGL. DEV. = 22.6 DEGREES REMARK 500 PRO A 153 C - N - CD ANGL. DEV. = -39.3 DEGREES REMARK 500 ILE A 203 CG1 - CB - CG2 ANGL. DEV. = -14.4 DEGREES REMARK 500 ARG A 206 CB - CA - C ANGL. DEV. = 21.6 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 ARG A 39 -151.28 -152.74 REMARK 500 ASP A 42 -157.67 -73.99 REMARK 500 THR A 43 -62.42 49.09 REMARK 500 GLU A 151 48.73 101.59 REMARK 500 GLU A 152 164.25 -46.65 REMARK 500 GLN A 154 178.20 -54.23 REMARK 500 ASP A 156 -116.79 -136.44 REMARK 500 GLU A 157 -148.08 -152.12 REMARK 500 ASP A 158 126.81 62.29 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 GLU A 149 GLU A 150 -130.44 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 ASP A 42 35.87 REMARK 500 GLU A 149 12.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2075 DISTANCE = 6.25 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BQS RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF MUCOSAL ADDRESSIN CELL ADHESION MOLECULE-1 REMARK 900 (MADCAM-1) REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE CONSTRUCT WAS DESIGNED WITH A C-TERMINAL XA CLEAVAGE REMARK 999 SITE THE C-TERMINAL FOUR RESIDUES ARE PART OF THIS CONSTRUCT DBREF 1GSM A -3 202 UNP Q13477 Q13477 19 224 DBREF 1GSM A 203 206 PDB 1GSM 1GSM 203 206 SEQADV 1GSM ASN A 94 UNP Q13477 ASP 116 CONFLICT SEQRES 1 A 210 GLN SER LEU GLN VAL LYS PRO LEU GLN VAL GLU PRO PRO SEQRES 2 A 210 GLU PRO VAL VAL ALA VAL ALA LEU GLY ALA SER ARG GLN SEQRES 3 A 210 LEU THR CYS ARG LEU ALA CYS ALA ASP ARG GLY ALA SER SEQRES 4 A 210 VAL GLN TRP ARG GLY LEU ASP THR SER LEU GLY ALA VAL SEQRES 5 A 210 GLN SER ASP THR GLY ARG SER VAL LEU THR VAL ARG ASN SEQRES 6 A 210 ALA SER LEU SER ALA ALA GLY THR ARG VAL CYS VAL GLY SEQRES 7 A 210 SER CYS GLY GLY ARG THR PHE GLN HIS THR VAL GLN LEU SEQRES 8 A 210 LEU VAL TYR ALA PHE PRO ASN GLN LEU THR VAL SER PRO SEQRES 9 A 210 ALA ALA LEU VAL PRO GLY ASP PRO GLU VAL ALA CYS THR SEQRES 10 A 210 ALA HIS LYS VAL THR PRO VAL ASP PRO ASN ALA LEU SER SEQRES 11 A 210 PHE SER LEU LEU VAL GLY GLY GLN GLU LEU GLU GLY ALA SEQRES 12 A 210 GLN ALA LEU GLY PRO GLU VAL GLN GLU GLU GLU GLU GLU SEQRES 13 A 210 PRO GLN GLY ASP GLU ASP VAL LEU PHE ARG VAL THR GLU SEQRES 14 A 210 ARG TRP ARG LEU PRO PRO LEU GLY THR PRO VAL PRO PRO SEQRES 15 A 210 ALA LEU TYR CYS GLN ALA THR MET ARG LEU PRO GLY LEU SEQRES 16 A 210 GLU LEU SER HIS ARG GLN ALA ILE PRO VAL LEU ILE GLU SEQRES 17 A 210 GLY ARG FORMUL 2 HOH *184(H2 O) HELIX 1 1 SER A 63 ALA A 67 5 5 SHEET 1 AA 3 LEU A 4 GLU A 7 0 SHEET 2 AA 3 ARG A 21 LEU A 27 -1 O THR A 24 N GLU A 7 SHEET 3 AA 3 ARG A 54 VAL A 59 -1 O SER A 55 N CYS A 25 SHEET 1 AB 5 VAL A 12 ALA A 16 0 SHEET 2 AB 5 ARG A 79 TYR A 90 1 O GLN A 86 N VAL A 13 SHEET 3 AB 5 GLY A 68 CYS A 76 -1 O GLY A 68 N LEU A 87 SHEET 4 AB 5 SER A 35 ARG A 39 -1 O SER A 35 N SER A 75 SHEET 5 AB 5 VAL A 48 ASP A 51 -1 O VAL A 48 N TRP A 38 SHEET 1 AC 4 GLN A 95 SER A 99 0 SHEET 2 AC 4 GLU A 109 VAL A 117 -1 O ALA A 111 N SER A 99 SHEET 3 AC 4 PHE A 161 ARG A 168 -1 O PHE A 161 N VAL A 117 SHEET 4 AC 4 GLN A 140 GLU A 148 -1 O GLN A 140 N ARG A 168 SHEET 1 AD 4 GLN A 134 GLU A 135 0 SHEET 2 AD 4 LEU A 125 VAL A 131 -1 O VAL A 131 N GLN A 134 SHEET 3 AD 4 ALA A 179 LEU A 188 -1 O TYR A 181 N LEU A 130 SHEET 4 AD 4 LEU A 191 PRO A 200 -1 O LEU A 191 N LEU A 188 SSBOND 1 CYS A 25 CYS A 72 1555 1555 2.03 SSBOND 2 CYS A 29 CYS A 76 1555 1555 2.01 SSBOND 3 CYS A 112 CYS A 182 1555 1555 2.07 CISPEP 1 GLU A 7 PRO A 8 0 -4.49 CISPEP 2 SER A 99 PRO A 100 0 -2.29 CISPEP 3 THR A 118 PRO A 119 0 -4.86 CISPEP 4 THR A 174 PRO A 175 0 5.78 CRYST1 64.000 99.200 70.500 90.00 90.00 90.00 C 2 2 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.015625 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010081 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014184 0.00000