HEADER SUGAR BINDING PROTEIN 22-FEB-07 2JHH TITLE STRUCTURE OF GLOBULAR HEADS OF M-FICOLIN AT ACIDIC PH COMPND MOL_ID: 1; COMPND 2 MOLECULE: FICOLIN-1; COMPND 3 CHAIN: C, F; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN, RESIDUES 109-326; COMPND 5 SYNONYM: FICOLIN-A, FICOLIN-ALPHA, M-FICOLIN, COLLAGEN/ FIBRINOGEN COMPND 6 DOMAIN-CONTAINING PROTEIN 1; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 7 EXPRESSION_SYSTEM_CELL_LINE: HIGH FIVE; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: BAC-TO-BAC SYTEM KEYWDS LECTIN, COLLAGEN, ACIDIC PH, COMPLEMENT, SUGAR-BINDING PROTEIN, KEYWDS 2 GLYCOPROTEIN, POLYMORPHISM, INNATE IMMUNITY, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR V.GARLATTI,L.MARTIN,E.GOUT,J.B.REISER,G.J.ARLAUD,N.M.THIELENS, AUTHOR 2 C.GABORIAUD REVDAT 6 09-OCT-24 2JHH 1 REMARK LINK REVDAT 5 03-APR-19 2JHH 1 SOURCE REVDAT 4 06-MAR-19 2JHH 1 JRNL REMARK REVDAT 3 24-FEB-09 2JHH 1 VERSN REVDAT 2 18-DEC-07 2JHH 1 JRNL REVDAT 1 09-OCT-07 2JHH 0 JRNL AUTH V.GARLATTI,L.MARTIN,E.GOUT,J.B.REISER,T.FUJITA,G.J.ARLAUD, JRNL AUTH 2 N.M.THIELENS,C.GABORIAUD JRNL TITL STRUCTURAL BASIS FOR INNATE IMMUNE SENSING BY M-FICOLIN AND JRNL TITL 2 ITS CONTROL BY A PH-DEPENDENT CONFORMATIONAL SWITCH. JRNL REF J. BIOL. CHEM. V. 282 35814 2007 JRNL REFN ISSN 0021-9258 JRNL PMID 17897951 JRNL DOI 10.1074/JBC.M705741200 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.03 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 43709 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) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2301 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3244 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2600 REMARK 3 BIN FREE R VALUE SET COUNT : 171 REMARK 3 BIN FREE R VALUE : 0.3000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3288 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 255 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.37000 REMARK 3 B22 (A**2) : 0.37000 REMARK 3 B33 (A**2) : -0.56000 REMARK 3 B12 (A**2) : 0.19000 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): 0.134 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.125 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.084 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.453 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3603 ; 0.009 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4911 ; 1.271 ; 1.913 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 461 ; 9.681 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 193 ;31.420 ;24.352 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 569 ;14.046 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;14.122 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 478 ; 0.113 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2896 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1509 ; 0.189 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2371 ; 0.300 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 159 ; 0.122 ; 0.200 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): 66 ; 0.224 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 17 ; 0.111 ; 0.200 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): 2238 ; 0.912 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3453 ; 1.322 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1612 ; 1.669 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1446 ; 2.292 ; 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 : 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. DISORDERED REGION ARE NOT MODELED REMARK 4 REMARK 4 2JHH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-FEB-07. REMARK 100 THE DEPOSITION ID IS D_1290031571. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-DEC-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.872 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45425 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 28.030 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.36900 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 5.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: C 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 350 REMARK 350 BIOMOLECULE: 2 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: F 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 C 80 REMARK 465 SER C 278 REMARK 465 ALA C 279 REMARK 465 ALA C 280 REMARK 465 LYS C 281 REMARK 465 GLY C 282 REMARK 465 TYR C 283 REMARK 465 LYS C 284 REMARK 465 TYR C 285 REMARK 465 SER C 286 REMARK 465 GLN F 80 REMARK 465 SER F 278 REMARK 465 ALA F 279 REMARK 465 ALA F 280 REMARK 465 LYS F 281 REMARK 465 GLY F 282 REMARK 465 TYR F 283 REMARK 465 LYS F 284 REMARK 465 TYR F 285 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 HOH C 2006 O HOH C 2007 1.95 REMARK 500 O PRO F 296 O HOH F 2128 2.04 REMARK 500 CD2 HIS F 222 O HOH F 2093 2.05 REMARK 500 CD LYS C 192 O HOH C 2090 2.06 REMARK 500 CE1 HIS F 222 O HOH F 2091 2.07 REMARK 500 CE1 HIS F 222 O HOH F 2092 2.07 REMARK 500 O LEU C 264 O HOH C 2122 2.08 REMARK 500 CB ALA C 83 O HOH C 2001 2.08 REMARK 500 CD2 HIS F 268 O HOH F 2122 2.09 REMARK 500 N ASN C 223 O HOH C 2095 2.09 REMARK 500 CE LYS F 244 O HOH F 2105 2.10 REMARK 500 O HOH F 2088 O HOH F 2093 2.11 REMARK 500 CG HIS F 222 O HOH F 2093 2.11 REMARK 500 O THR C 220 O HOH C 2095 2.11 REMARK 500 O LEU F 219 O HOH F 2088 2.11 REMARK 500 O HOH F 2051 O HOH F 2076 2.12 REMARK 500 CG1 VAL C 206 O HOH C 2096 2.13 REMARK 500 O LEU F 264 O HOH F 2117 2.13 REMARK 500 O HOH C 2081 O HOH C 2082 2.14 REMARK 500 N HIS C 222 O HOH C 2095 2.16 REMARK 500 CD2 TYR F 106 O HOH F 2007 2.16 REMARK 500 CB HIS F 268 O HOH F 2120 2.16 REMARK 500 SD MET F 265 O HOH F 2047 2.16 REMARK 500 O HOH C 2006 O HOH C 2009 2.17 REMARK 500 CA PHE C 182 O HOH C 2075 2.18 REMARK 500 CB ALA F 83 O HOH F 2003 2.19 REMARK 500 CA PRO C 86 O HOH C 2005 2.19 REMARK 500 O HOH C 2107 O HOH C 2111 2.19 REMARK 500 O GLY C 85 O HOH C 2005 2.19 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 SER C 257 CA SER C 257 C 0.825 REMARK 500 SER C 257 C SER C 257 O 0.156 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 PHE C 245 N - CA - C ANGL. DEV. = 26.9 DEGREES REMARK 500 SER C 257 CB - CA - C ANGL. DEV. = -15.2 DEGREES REMARK 500 SER C 257 CA - C - O ANGL. DEV. = -44.3 DEGREES REMARK 500 SER C 257 CA - C - N ANGL. DEV. = -39.6 DEGREES REMARK 500 ASN C 258 C - N - CA ANGL. DEV. = -27.1 DEGREES REMARK 500 PHE F 245 N - CA - C ANGL. DEV. = 24.7 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 C 88 -175.39 -170.18 REMARK 500 MET C 133 -27.26 -151.20 REMARK 500 MET C 133 -1.36 -158.62 REMARK 500 ASP C 134 -3.03 -143.22 REMARK 500 ASP C 134 -3.03 -157.91 REMARK 500 PHE C 245 -3.67 -52.90 REMARK 500 ALA C 252 -94.31 -116.84 REMARK 500 MET F 133 -30.71 -150.66 REMARK 500 MET F 133 1.46 -160.41 REMARK 500 ASP F 134 -5.31 -145.80 REMARK 500 ASP F 134 -5.31 -160.77 REMARK 500 THR F 220 77.89 -116.55 REMARK 500 HIS F 222 62.60 -65.15 REMARK 500 HIS F 222 63.67 -66.26 REMARK 500 ALA F 252 -89.71 -110.17 REMARK 500 CYS F 254 30.89 80.66 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 LYS C 244 PHE C 245 122.60 REMARK 500 LYS F 244 PHE F 245 120.36 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 SER C 257 34.83 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 C 400 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP C 233 OD1 REMARK 620 2 ASP C 233 OD2 50.6 REMARK 620 3 ASP C 235 OD1 76.6 116.7 REMARK 620 4 SER C 237 O 152.6 156.4 83.6 REMARK 620 5 SER C 239 O 115.6 82.4 94.1 84.1 REMARK 620 6 HOH C2108 O 80.3 112.3 85.6 79.6 163.6 REMARK 620 7 HOH C2110 O 114.8 81.9 160.3 79.9 94.8 80.9 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA F 400 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP F 233 OD2 REMARK 620 2 ASP F 233 OD1 50.2 REMARK 620 3 ASP F 235 OD1 115.6 76.7 REMARK 620 4 SER F 237 O 157.9 151.5 83.3 REMARK 620 5 SER F 239 O 82.9 117.2 94.7 84.1 REMARK 620 6 HOH F2101 O 113.2 78.1 82.3 79.3 163.4 REMARK 620 7 HOH F2102 O 83.0 120.4 161.2 78.0 84.4 93.2 REMARK 620 N 1 2 3 4 5 6 REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA C 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA F 400 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2JHI RELATED DB: PDB REMARK 900 STRUCTURE OF GLOBULAR HEADS OF M-FICOLIN COMPLEXED WITH N-ACETYL-D- REMARK 900 GALACTOSAMINE REMARK 900 RELATED ID: 2JHK RELATED DB: PDB REMARK 900 STRUCTURE OF GLOBULAR HEADS OF M-FICOLIN COMPLEXED WITH N-ACETYL-D- REMARK 900 GLUCOSAMINE REMARK 900 RELATED ID: 2JHL RELATED DB: PDB REMARK 900 STRUCTURE OF GLOBULAR HEADS OF M-FICOLIN COMPLEXED WITH SIALIC ACID REMARK 900 RELATED ID: 2JHM RELATED DB: PDB REMARK 900 STRUCTURE OF GLOBULAR HEADS OF M-FICOLIN AT NEUTRAL PH DBREF 2JHH C 80 297 UNP O00602 FCN1_HUMAN 109 326 DBREF 2JHH F 80 297 UNP O00602 FCN1_HUMAN 109 326 SEQADV 2JHH THR C 177 UNP O00602 VAL 206 CONFLICT SEQADV 2JHH THR F 177 UNP O00602 VAL 206 CONFLICT SEQRES 1 C 218 GLN SER CYS ALA THR GLY PRO ARG ASN CYS LYS ASP LEU SEQRES 2 C 218 LEU ASP ARG GLY TYR PHE LEU SER GLY TRP HIS THR ILE SEQRES 3 C 218 TYR LEU PRO ASP CYS ARG PRO LEU THR VAL LEU CYS ASP SEQRES 4 C 218 MET ASP THR ASP GLY GLY GLY TRP THR VAL PHE GLN ARG SEQRES 5 C 218 ARG MET ASP GLY SER VAL ASP PHE TYR ARG ASP TRP ALA SEQRES 6 C 218 ALA TYR LYS GLN GLY PHE GLY SER GLN LEU GLY GLU PHE SEQRES 7 C 218 TRP LEU GLY ASN ASP ASN ILE HIS ALA LEU THR ALA GLN SEQRES 8 C 218 GLY SER SER GLU LEU ARG THR ASP LEU VAL ASP PHE GLU SEQRES 9 C 218 GLY ASN HIS GLN PHE ALA LYS TYR LYS SER PHE LYS VAL SEQRES 10 C 218 ALA ASP GLU ALA GLU LYS TYR LYS LEU VAL LEU GLY ALA SEQRES 11 C 218 PHE VAL GLY GLY SER ALA GLY ASN SER LEU THR GLY HIS SEQRES 12 C 218 ASN ASN ASN PHE PHE SER THR LYS ASP GLN ASP ASN ASP SEQRES 13 C 218 VAL SER SER SER ASN CYS ALA GLU LYS PHE GLN GLY ALA SEQRES 14 C 218 TRP TRP TYR ALA ASP CYS HIS ALA SER ASN LEU ASN GLY SEQRES 15 C 218 LEU TYR LEU MET GLY PRO HIS GLU SER TYR ALA ASN GLY SEQRES 16 C 218 ILE ASN TRP SER ALA ALA LYS GLY TYR LYS TYR SER TYR SEQRES 17 C 218 LYS VAL SER GLU MET LYS VAL ARG PRO ALA SEQRES 1 F 218 GLN SER CYS ALA THR GLY PRO ARG ASN CYS LYS ASP LEU SEQRES 2 F 218 LEU ASP ARG GLY TYR PHE LEU SER GLY TRP HIS THR ILE SEQRES 3 F 218 TYR LEU PRO ASP CYS ARG PRO LEU THR VAL LEU CYS ASP SEQRES 4 F 218 MET ASP THR ASP GLY GLY GLY TRP THR VAL PHE GLN ARG SEQRES 5 F 218 ARG MET ASP GLY SER VAL ASP PHE TYR ARG ASP TRP ALA SEQRES 6 F 218 ALA TYR LYS GLN GLY PHE GLY SER GLN LEU GLY GLU PHE SEQRES 7 F 218 TRP LEU GLY ASN ASP ASN ILE HIS ALA LEU THR ALA GLN SEQRES 8 F 218 GLY SER SER GLU LEU ARG THR ASP LEU VAL ASP PHE GLU SEQRES 9 F 218 GLY ASN HIS GLN PHE ALA LYS TYR LYS SER PHE LYS VAL SEQRES 10 F 218 ALA ASP GLU ALA GLU LYS TYR LYS LEU VAL LEU GLY ALA SEQRES 11 F 218 PHE VAL GLY GLY SER ALA GLY ASN SER LEU THR GLY HIS SEQRES 12 F 218 ASN ASN ASN PHE PHE SER THR LYS ASP GLN ASP ASN ASP SEQRES 13 F 218 VAL SER SER SER ASN CYS ALA GLU LYS PHE GLN GLY ALA SEQRES 14 F 218 TRP TRP TYR ALA ASP CYS HIS ALA SER ASN LEU ASN GLY SEQRES 15 F 218 LEU TYR LEU MET GLY PRO HIS GLU SER TYR ALA ASN GLY SEQRES 16 F 218 ILE ASN TRP SER ALA ALA LYS GLY TYR LYS TYR SER TYR SEQRES 17 F 218 LYS VAL SER GLU MET LYS VAL ARG PRO ALA HET CA C 400 1 HET CA F 400 1 HETNAM CA CALCIUM ION FORMUL 3 CA 2(CA 2+) FORMUL 5 HOH *255(H2 O) HELIX 1 1 ASN C 88 ARG C 95 1 8 HELIX 2 2 ASP C 120 GLY C 124 5 5 HELIX 3 3 ASP C 142 GLY C 149 1 8 HELIX 4 4 GLY C 160 GLN C 170 1 11 HELIX 5 5 ASP C 198 LYS C 202 5 5 HELIX 6 6 LEU C 219 ASN C 223 5 5 HELIX 7 7 ASN C 240 PHE C 245 1 6 HELIX 8 8 ASN F 88 ARG F 95 1 8 HELIX 9 9 ASP F 120 GLY F 124 5 5 HELIX 10 10 ASP F 142 GLY F 149 1 8 HELIX 11 11 GLY F 160 GLN F 170 1 11 HELIX 12 12 ASP F 198 LYS F 202 5 5 HELIX 13 13 ASN F 240 PHE F 245 1 6 SHEET 1 CA 7 GLY C 101 TYR C 106 0 SHEET 2 CA 7 PRO C 112 ASP C 118 -1 O LEU C 113 N ILE C 105 SHEET 3 CA 7 TRP C 126 ARG C 132 -1 O TRP C 126 N ASP C 118 SHEET 4 CA 7 VAL C 289 PRO C 296 -1 O SER C 290 N ARG C 132 SHEET 5 CA 7 SER C 173 VAL C 180 -1 O GLU C 174 N ARG C 295 SHEET 6 CA 7 HIS C 186 TYR C 191 -1 O GLN C 187 N LEU C 179 SHEET 7 CA 7 PHE C 210 GLY C 212 -1 N VAL C 211 O LYS C 190 SHEET 1 CB 5 GLY C 101 TYR C 106 0 SHEET 2 CB 5 PRO C 112 ASP C 118 -1 O LEU C 113 N ILE C 105 SHEET 3 CB 5 TRP C 126 ARG C 132 -1 O TRP C 126 N ASP C 118 SHEET 4 CB 5 PHE C 157 TRP C 158 -1 O PHE C 157 N ARG C 131 SHEET 5 CB 5 PHE C 150 GLY C 151 -1 O PHE C 150 N TRP C 158 SHEET 1 CC 2 PHE C 194 VAL C 196 0 SHEET 2 CC 2 LEU C 205 LEU C 207 -1 O VAL C 206 N LYS C 195 SHEET 1 CD 2 LEU C 264 MET C 265 0 SHEET 2 CD 2 ASN C 273 GLY C 274 -1 O GLY C 274 N LEU C 264 SHEET 1 FA 7 GLY F 101 TYR F 106 0 SHEET 2 FA 7 PRO F 112 ASP F 118 -1 O LEU F 113 N ILE F 105 SHEET 3 FA 7 TRP F 126 ARG F 132 -1 O TRP F 126 N ASP F 118 SHEET 4 FA 7 TYR F 287 PRO F 296 -1 O SER F 290 N ARG F 132 SHEET 5 FA 7 SER F 173 ASP F 181 -1 O GLU F 174 N ARG F 295 SHEET 6 FA 7 HIS F 186 TYR F 191 -1 O GLN F 187 N LEU F 179 SHEET 7 FA 7 PHE F 210 GLY F 212 -1 N VAL F 211 O LYS F 190 SHEET 1 FB 5 GLY F 101 TYR F 106 0 SHEET 2 FB 5 PRO F 112 ASP F 118 -1 O LEU F 113 N ILE F 105 SHEET 3 FB 5 TRP F 126 ARG F 132 -1 O TRP F 126 N ASP F 118 SHEET 4 FB 5 PHE F 157 TRP F 158 -1 O PHE F 157 N ARG F 131 SHEET 5 FB 5 PHE F 150 GLY F 151 -1 O PHE F 150 N TRP F 158 SHEET 1 FC 2 PHE F 194 VAL F 196 0 SHEET 2 FC 2 LEU F 205 LEU F 207 -1 O VAL F 206 N LYS F 195 SHEET 1 FD 2 LEU F 264 MET F 265 0 SHEET 2 FD 2 ASN F 273 GLY F 274 -1 O GLY F 274 N LEU F 264 SSBOND 1 CYS C 82 CYS C 110 1555 1555 2.04 SSBOND 2 CYS C 89 CYS C 117 1555 1555 2.06 SSBOND 3 CYS C 241 CYS C 254 1555 1555 2.03 SSBOND 4 CYS F 82 CYS F 110 1555 1555 2.04 SSBOND 5 CYS F 89 CYS F 117 1555 1555 2.06 SSBOND 6 CYS F 241 CYS F 254 1555 1555 2.04 LINK OD1 ASP C 233 CA CA C 400 1555 1555 2.60 LINK OD2 ASP C 233 CA CA C 400 1555 1555 2.50 LINK OD1 ASP C 235 CA CA C 400 1555 1555 2.27 LINK O SER C 237 CA CA C 400 1555 1555 2.41 LINK O SER C 239 CA CA C 400 1555 1555 2.47 LINK CA CA C 400 O HOH C2108 1555 1555 2.32 LINK CA CA C 400 O HOH C2110 1555 1555 2.31 LINK OD2 ASP F 233 CA CA F 400 1555 1555 2.53 LINK OD1 ASP F 233 CA CA F 400 1555 1555 2.62 LINK OD1 ASP F 235 CA CA F 400 1555 1555 2.21 LINK O SER F 237 CA CA F 400 1555 1555 2.43 LINK O SER F 239 CA CA F 400 1555 1555 2.51 LINK CA CA F 400 O HOH F2101 1555 1555 2.46 LINK CA CA F 400 O HOH F2102 1555 1555 2.39 CISPEP 1 THR F 220 GLY F 221 0 -4.07 SITE 1 AC1 6 ASP C 233 ASP C 235 SER C 237 SER C 239 SITE 2 AC1 6 HOH C2108 HOH C2110 SITE 1 AC2 6 ASP F 233 ASP F 235 SER F 237 SER F 239 SITE 2 AC2 6 HOH F2101 HOH F2102 CRYST1 69.400 69.400 77.630 90.00 90.00 120.00 P 3 6 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 0.014409 0.008319 0.000000 0.00000 SCALE2 0.000000 0.016638 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012882 0.00000