HEADER TRANSPORT PROTEIN 19-JUN-07 2V3N TITLE CRYSTALLOGRAPHIC ANALYSIS OF UPPER AXIAL LIGAND SUBSTITUTIONS IN TITLE 2 COBALAMIN BOUND TO TRANSCOBALAMIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCOBALAMIN-2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TRANSCOBALAMIN II; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: BOVINE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 ORGAN: BLOOD; SOURCE 6 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: SMD 1168; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PPICZ(ALPHA)-LB KEYWDS TRANSPORT PROTEIN, COBALT, TRANSPORT, GLYCOPROTEIN, ION TRANSPORT, KEYWDS 2 VITAMIN B12 TRANSPORT PROTEIN, COBALT TRANSPORT, BETA LIGAND KEYWDS 3 SUBSTITUTION EXPDTA X-RAY DIFFRACTION AUTHOR J.WUERGES,S.GEREMIA,L.RANDACCIO REVDAT 6 13-DEC-23 2V3N 1 REMARK REVDAT 5 31-OCT-12 2V3N 1 FORMUL REVDAT 4 13-JUL-11 2V3N 1 VERSN REVDAT 3 24-FEB-09 2V3N 1 VERSN REVDAT 2 15-APR-08 2V3N 1 REMARK HETATM CONECT MASTER REVDAT 1 30-OCT-07 2V3N 0 JRNL AUTH J.WUERGES,S.GEREMIA,S.N.FEDOSOV,L.RANDACCIO JRNL TITL VITAMIN B12 TRANSPORT PROTEINS: CRYSTALLOGRAPHIC ANALYSIS OF JRNL TITL 2 BETA-AXIAL LIGAND SUBSTITUTIONS IN COBALAMIN BOUND TO JRNL TITL 3 TRANSCOBALAMIN. JRNL REF IUBMB LIFE V. 59 722 2007 JRNL REFN ISSN 1521-6543 JRNL PMID 17943552 JRNL DOI 10.1080/15216540701673413 REMARK 2 REMARK 2 RESOLUTION. 2.73 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.3.0037 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) : 2.73 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 20574 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) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.250 REMARK 3 FREE R VALUE TEST SET COUNT : 857 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.73 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.80 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1429 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3460 REMARK 3 BIN FREE R VALUE SET COUNT : 59 REMARK 3 BIN FREE R VALUE : 0.3860 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3178 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 96 REMARK 3 SOLVENT ATOMS : 174 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.43300 REMARK 3 B22 (A**2) : 0.43300 REMARK 3 B33 (A**2) : -0.64900 REMARK 3 B12 (A**2) : 0.21600 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): 0.448 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.291 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.212 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 19.725 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.928 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.898 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3352 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4570 ; 1.308 ; 2.024 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 405 ; 5.771 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 143 ;37.867 ;23.776 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 589 ;17.011 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;20.715 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 507 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2516 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1550 ; 0.207 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2293 ; 0.305 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 173 ; 0.143 ; 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): 33 ; 0.255 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.225 ; 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): 2081 ; 0.661 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3254 ; 1.181 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1418 ; 1.319 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1315 ; 2.275 ; 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1001 A 1001 REMARK 3 ORIGIN FOR THE GROUP (A): 13.3803 38.4602 16.7576 REMARK 3 T TENSOR REMARK 3 T11: -0.0049 T22: -0.0868 REMARK 3 T33: 0.0914 T12: 0.0497 REMARK 3 T13: -0.0250 T23: -0.0405 REMARK 3 L TENSOR REMARK 3 L11: 4.3901 L22: 2.0372 REMARK 3 L33: 8.2135 L12: 1.7518 REMARK 3 L13: -1.0918 L23: -1.4036 REMARK 3 S TENSOR REMARK 3 S11: 0.0246 S12: 0.1984 S13: -0.3412 REMARK 3 S21: -0.3786 S22: -0.0073 S23: 0.2976 REMARK 3 S31: 0.2415 S32: -0.2478 S33: -0.0173 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 302 REMARK 3 ORIGIN FOR THE GROUP (A): 4.0206 48.0700 19.5369 REMARK 3 T TENSOR REMARK 3 T11: -0.0728 T22: -0.0450 REMARK 3 T33: -0.0273 T12: 0.0706 REMARK 3 T13: 0.0672 T23: -0.0298 REMARK 3 L TENSOR REMARK 3 L11: 0.8259 L22: 2.1086 REMARK 3 L33: 3.1154 L12: -0.2107 REMARK 3 L13: 0.1690 L23: 0.4702 REMARK 3 S TENSOR REMARK 3 S11: -0.0464 S12: 0.0667 S13: -0.0492 REMARK 3 S21: 0.1552 S22: -0.0882 S23: 0.2228 REMARK 3 S31: -0.0606 S32: -0.2868 S33: 0.1346 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 303 A 314 REMARK 3 ORIGIN FOR THE GROUP (A): 32.2790 46.4688 40.2227 REMARK 3 T TENSOR REMARK 3 T11: 0.5667 T22: 0.8740 REMARK 3 T33: 0.7301 T12: 0.7923 REMARK 3 T13: -0.1198 T23: -0.0526 REMARK 3 L TENSOR REMARK 3 L11: 48.5432 L22: 111.4766 REMARK 3 L33: 0.0027 L12: -73.5624 REMARK 3 L13: 0.3596 L23: -0.5450 REMARK 3 S TENSOR REMARK 3 S11: -1.4201 S12: -0.9039 S13: 4.3013 REMARK 3 S21: 1.5375 S22: 1.8051 S23: -2.7827 REMARK 3 S31: 0.9630 S32: -0.9500 S33: -0.3850 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 315 A 414 REMARK 3 ORIGIN FOR THE GROUP (A): 26.4743 31.6496 17.6555 REMARK 3 T TENSOR REMARK 3 T11: 0.0326 T22: -0.0983 REMARK 3 T33: -0.0440 T12: 0.1121 REMARK 3 T13: -0.0064 T23: -0.0087 REMARK 3 L TENSOR REMARK 3 L11: 3.2899 L22: 2.9285 REMARK 3 L33: 2.6865 L12: -1.2088 REMARK 3 L13: -0.2627 L23: 0.6285 REMARK 3 S TENSOR REMARK 3 S11: -0.0575 S12: 0.1582 S13: -0.0783 REMARK 3 S21: -0.0222 S22: -0.0108 S23: 0.0788 REMARK 3 S31: 0.2290 S32: 0.1060 S33: 0.0684 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT 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. AMINO ACIDS FROM LYS168 TO VAL176 WERE NOT MODELLED REMARK 3 DUE TO DISORDER. HIS175 AS UPPER AXIAL LIGAND OF COBALAMIN HAS REMARK 3 BEEN DISPLACED BY EXTERNALLY SUPPLIED CYANIDE. REMARK 4 REMARK 4 2V3N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-JUN-07. REMARK 100 THE DEPOSITION ID IS D_1290032961. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-APR-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 5.2R REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(220) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21370 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 20.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.75000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: PDB ENTRY 2BBC REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN AT 0.5 MM IN 1 M NACL, 0.1 M REMARK 280 TRIS, PH 7.5 CRYSTALLIZED FROM 28% PEG 8000, 0.2 M MAGNESIUM REMARK 280 ACETATE, 0.1 M TRIS PH 8.5, 20% 2-METHYL-2, 4-PENTADIOL, 15 MM REMARK 280 KCN REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 43.40500 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 86.81000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 86.81000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 43.40500 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 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 LYS A 168 REMARK 465 PRO A 169 REMARK 465 HIS A 170 REMARK 465 LEU A 171 REMARK 465 LEU A 172 REMARK 465 GLN A 173 REMARK 465 ASP A 174 REMARK 465 HIS A 175 REMARK 465 VAL A 176 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 314 C PRO A 314 O 0.181 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 ALA A 47 58.28 -106.00 REMARK 500 PRO A 69 161.20 -40.89 REMARK 500 LYS A 73 93.61 -64.99 REMARK 500 ASP A 75 -40.65 -147.60 REMARK 500 ASP A 77 -66.08 -163.77 REMARK 500 SER A 78 105.11 -8.91 REMARK 500 GLU A 79 84.93 77.04 REMARK 500 HIS A 126 -83.34 18.54 REMARK 500 THR A 134 -91.99 -92.45 REMARK 500 SER A 241 -120.18 45.54 REMARK 500 LEU A 242 12.73 52.81 REMARK 500 ARG A 243 46.15 -156.22 REMARK 500 GLU A 306 13.51 -152.86 REMARK 500 THR A 307 103.50 -35.54 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 PRO A 314 -11.15 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 B12 A1001 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYN A1002 C REMARK 620 2 B12 A1001 N21 90.2 REMARK 620 3 B12 A1001 N22 89.3 90.1 REMARK 620 4 B12 A1001 N23 88.3 173.4 96.4 REMARK 620 5 B12 A1001 N24 86.3 83.4 172.1 90.1 REMARK 620 N 1 2 3 4 REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE B12 A1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CYN A1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A1416 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A1417 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A1418 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BB6 RELATED DB: PDB REMARK 900 STRUCTURE OF COBALAMIN-COMPLEXED BOVINE TRANSCOBALAMIN INMONOCLINIC REMARK 900 CRYSTAL FORM REMARK 900 RELATED ID: 2V3P RELATED DB: PDB REMARK 900 CRYSTALLOGRAPHIC ANALYSIS OF BETA-AXIAL LIGAND SUBSTITUTIONS IN REMARK 900 COBALAMIN BOUND TO TRANSCOBALAMIN REMARK 900 RELATED ID: 2BBC RELATED DB: PDB REMARK 900 STRUCTURE OF COBALAMIN-COMPLEXED BOVINE TRANSCOBALAMIN INTRIGONAL REMARK 900 CRYSTAL FORM DBREF 2V3N A 1 414 UNP Q9XSC9 TCO2_BOVIN 19 432 SEQRES 1 A 414 ASN ILE CYS GLU ILE THR GLU VAL ASP SER THR LEU VAL SEQRES 2 A 414 GLU ARG LEU GLY GLN ARG LEU LEU PRO TRP MET ASP ARG SEQRES 3 A 414 LEU SER GLN GLU GLN LEU ASN PRO SER ILE TYR VAL GLY SEQRES 4 A 414 LEU ARG LEU SER SER LEU GLN ALA GLY ALA LYS GLU ALA SEQRES 5 A 414 HIS TYR LEU HIS SER LEU LYS LEU SER TYR GLN GLN SER SEQRES 6 A 414 LEU LEU ARG PRO ALA SER ASN LYS ASP ASP ASN ASP SER SEQRES 7 A 414 GLU ALA LYS PRO SER MET GLY GLN LEU ALA LEU TYR LEU SEQRES 8 A 414 LEU ALA LEU ARG ALA ASN CYS GLU PHE ILE GLY GLY ARG SEQRES 9 A 414 LYS GLY ASP ARG LEU VAL SER GLN LEU LYS ARG PHE LEU SEQRES 10 A 414 GLU ASP GLU LYS ARG ALA ILE GLY HIS ASN HIS GLN GLY SEQRES 11 A 414 HIS PRO ARG THR SER TYR TYR GLN TYR SER LEU GLY ILE SEQRES 12 A 414 LEU ALA LEU CYS VAL HIS GLN LYS ARG VAL HIS ASP SER SEQRES 13 A 414 VAL VAL GLY LYS LEU LEU TYR ALA VAL GLU HIS LYS PRO SEQRES 14 A 414 HIS LEU LEU GLN ASP HIS VAL SER VAL ASP THR MET ALA SEQRES 15 A 414 MET ALA GLY MET ALA PHE SER CYS LEU GLU LEU SER ASN SEQRES 16 A 414 LEU ASN PRO LYS GLN ARG ASN ARG ILE ASN LEU ALA LEU SEQRES 17 A 414 LYS ARG VAL GLN GLU LYS ILE LEU LYS ALA GLN THR PRO SEQRES 18 A 414 GLU GLY TYR PHE GLY ASN VAL TYR SER THR PRO LEU ALA SEQRES 19 A 414 LEU GLN LEU LEU MET GLY SER LEU ARG PRO SER VAL GLU SEQRES 20 A 414 LEU GLY THR ALA CYS LEU LYS ALA LYS ALA ALA LEU GLN SEQRES 21 A 414 ALA SER LEU GLN HIS LYS THR PHE GLN ASN PRO LEU MET SEQRES 22 A 414 ILE SER GLN LEU LEU PRO VAL LEU ASN GLN LYS SER TYR SEQRES 23 A 414 VAL ASP LEU ILE SER PRO ASP CYS GLN ALA PRO ARG ALA SEQRES 24 A 414 LEU LEU GLU PRO ALA LEU GLU THR PRO PRO GLN ALA LYS SEQRES 25 A 414 VAL PRO LYS PHE ILE ASP VAL LEU LEU LYS VAL SER GLY SEQRES 26 A 414 ILE SER PRO SER TYR ARG HIS SER VAL SER VAL PRO ALA SEQRES 27 A 414 GLY SER SER LEU GLU ASP ILE LEU LYS ASN ALA GLN GLU SEQRES 28 A 414 HIS GLY ARG PHE ARG PHE ARG THR GLN ALA SER LEU SER SEQRES 29 A 414 GLY PRO PHE LEU THR SER VAL LEU GLY ARG LYS ALA GLY SEQRES 30 A 414 GLU ARG GLU PHE TRP GLN VAL LEU ARG ASP PRO ASP THR SEQRES 31 A 414 PRO LEU GLN GLN GLY ILE ALA ASP TYR ARG PRO LYS ASP SEQRES 32 A 414 GLY GLU THR ILE GLU LEU ARG LEU VAL GLY TRP HET B12 A1001 91 HET CYN A1002 2 HET CL A1416 1 HET CL A1417 1 HET CL A1418 1 HETNAM B12 COBALAMIN HETNAM CYN CYANIDE ION HETNAM CL CHLORIDE ION FORMUL 2 B12 C62 H89 CO N13 O14 P 2+ FORMUL 3 CYN C N 1- FORMUL 4 CL 3(CL 1-) FORMUL 7 HOH *174(H2 O) HELIX 1 1 ASP A 9 ARG A 26 1 18 HELIX 2 2 ASN A 33 SER A 43 1 11 HELIX 3 3 ALA A 49 LEU A 67 1 19 HELIX 4 4 SER A 83 ASN A 97 1 15 HELIX 5 5 GLY A 102 GLY A 125 1 24 HELIX 6 6 SER A 135 VAL A 148 1 14 HELIX 7 7 VAL A 153 GLU A 166 1 14 HELIX 8 8 SER A 177 ASN A 195 1 19 HELIX 9 9 GLN A 200 ALA A 218 1 19 HELIX 10 10 SER A 230 MET A 239 1 10 HELIX 11 11 SER A 245 GLN A 264 1 20 HELIX 12 12 ASN A 270 ASN A 282 1 13 HELIX 13 13 SER A 285 SER A 291 5 7 HELIX 14 14 SER A 341 HIS A 352 1 12 SHEET 1 AA 5 TYR A 330 ALA A 338 0 SHEET 2 AA 5 LYS A 315 VAL A 323 -1 N VAL A 319 O VAL A 334 SHEET 3 AA 5 GLU A 405 GLY A 413 1 O ILE A 407 N LYS A 322 SHEET 4 AA 5 GLU A 380 ARG A 386 -1 N GLN A 383 O ARG A 410 SHEET 5 AA 5 THR A 390 LEU A 392 -1 O THR A 390 N ARG A 386 SHEET 1 AB 3 ARG A 356 SER A 362 0 SHEET 2 AB 3 GLY A 365 VAL A 371 -1 O PHE A 367 N GLN A 360 SHEET 3 AB 3 ARG A 374 ALA A 376 -1 O ARG A 374 N VAL A 371 SSBOND 1 CYS A 3 CYS A 252 1555 1555 2.04 SSBOND 2 CYS A 98 CYS A 294 1555 1555 2.06 SSBOND 3 CYS A 147 CYS A 190 1555 1555 2.05 LINK CO B12 A1001 C CYN A1002 1555 1555 1.89 CISPEP 1 SER A 327 PRO A 328 0 1.34 CISPEP 2 ASP A 387 PRO A 388 0 0.51 SITE 1 AC1 37 GLY A 85 GLN A 86 THR A 134 TYR A 137 SITE 2 AC1 37 GLN A 138 ASP A 179 ASN A 227 TYR A 229 SITE 3 AC1 37 SER A 230 LEU A 233 MET A 273 GLN A 276 SITE 4 AC1 37 SER A 362 LEU A 363 SER A 364 GLY A 365 SITE 5 AC1 37 PRO A 366 PHE A 367 LEU A 368 PHE A 381 SITE 6 AC1 37 TRP A 382 GLN A 383 VAL A 384 LEU A 392 SITE 7 AC1 37 GLN A 393 GLY A 395 TRP A 414 CYN A1002 SITE 8 AC1 37 CL A1416 HOH A2085 HOH A2133 HOH A2169 SITE 9 AC1 37 HOH A2170 HOH A2171 HOH A2172 HOH A2173 SITE 10 AC1 37 HOH A2174 SITE 1 AC2 1 B12 A1001 SITE 1 AC3 6 TYR A 229 THR A 267 GLN A 269 ASN A 270 SITE 2 AC3 6 GLN A 394 B12 A1001 SITE 1 AC4 6 ARG A 356 PHE A 357 ARG A 358 SER A 370 SITE 2 AC4 6 LEU A 372 GLY A 373 SITE 1 AC5 3 ARG A 108 GLN A 112 HOH A2034 CRYST1 100.830 100.830 130.215 90.00 90.00 120.00 P 31 2 1 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 0.009918 0.005726 0.000000 0.00000 SCALE2 0.000000 0.011452 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007680 0.00000