HEADER SIGNALING PROTEIN 31-AUG-12 4B92 TITLE CRYSTAL STRUCTURE OF TRUNCATED HUMAN CRMP-5 SOAKED WITH ZN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROPYRIMIDINASE-RELATED PROTEIN 5; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 1-483; COMPND 5 SYNONYM: DRP-5, CRMP3-ASSOCIATED MOLECULE, CRAM, COLLAPSIN RESPONSE COMPND 6 MEDIATOR PROTEIN 5, CRMP-5, UNC33-LIKE PHOSPHOPROTEIN 6, ULIP-6; 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: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PNIC-BSA4; SOURCE 11 OTHER_DETAILS: MAMMALIAN GENE COLLECTION (MGC) KEYWDS SIGNALING PROTEIN, NEUROGENESIS, PHOSPHOPROTEIN, CRMP, TIM BARREL, KEYWDS 2 AXONAL OUTGROWTH, DEVELOPMENTAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.PONNUSAMY,B.LOHKAMP REVDAT 4 20-DEC-23 4B92 1 REMARK LINK REVDAT 3 25-SEP-13 4B92 1 REMARK REVDAT 2 19-JUN-13 4B92 1 JRNL REVDAT 1 13-FEB-13 4B92 0 JRNL AUTH R.PONNUSAMY,B.LOHKAMP JRNL TITL INSIGHTS INTO THE OLIGOMERIZATION OF CRMPS: CRYSTAL JRNL TITL 2 STRUCTURE OF HUMAN COLLAPSIN RESPONSE MEDIATOR PROTEIN 5. JRNL REF J.NEUROCHEM. V. 125 855 2013 JRNL REFN ISSN 0022-3042 JRNL PMID 23373749 JRNL DOI 10.1111/JNC.12188 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.92 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 21826 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) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.191 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 : 1180 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) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.98 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1547 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.88 REMARK 3 BIN R VALUE (WORKING SET) : 0.2770 REMARK 3 BIN FREE R VALUE SET COUNT : 98 REMARK 3 BIN FREE R VALUE : 0.3410 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7300 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 3 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 70.55 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.19000 REMARK 3 B22 (A**2) : -2.19000 REMARK 3 B33 (A**2) : 4.37000 REMARK 3 B12 (A**2) : 0.00000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.428 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.306 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 16.594 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.933 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.877 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7452 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 7166 ; 0.005 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10102 ; 1.459 ; 1.952 REMARK 3 BOND ANGLES OTHERS (DEGREES): 16490 ; 1.014 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 949 ; 6.414 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 310 ;32.011 ;24.065 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1267 ;15.949 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 42 ;15.570 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1167 ; 0.072 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8401 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1637 ; 0.005 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 8 481 B 8 481 29976 0.10 0.05 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 : 1.20 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. U VALUES REFINED INDIVIDUALLY REMARK 4 REMARK 4 4B92 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1290053859. 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 REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.03873 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23108 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 39.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.14000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : 0.65000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 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: PDB ENTRY 4B91 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 23% (V/V) PEG 400 MMT PH 5.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+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 123.23000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 44.75000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 44.75000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 61.61500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 44.75000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 44.75000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 184.84500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 44.75000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.75000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 61.61500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 44.75000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.75000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 184.84500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 123.23000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 61200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -274.8 KCAL/MOL 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 350 BIOMT1 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 123.23000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 44.75000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 -44.75000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 61.61500 REMARK 350 BIOMT1 4 0.000000 -1.000000 0.000000 44.75000 REMARK 350 BIOMT2 4 1.000000 0.000000 0.000000 -44.75000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 61.61500 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 61200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -274.8 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 3 0.000000 1.000000 0.000000 44.75000 REMARK 350 BIOMT2 3 -1.000000 0.000000 0.000000 44.75000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 -61.61500 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 44.75000 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 44.75000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 61.61500 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 SER A 0 REMARK 465 MET A 1 REMARK 465 LEU A 2 REMARK 465 ALA A 3 REMARK 465 ASN A 4 REMARK 465 SER A 5 REMARK 465 ALA A 6 REMARK 465 LYS A 483 REMARK 465 SER B 0 REMARK 465 MET B 1 REMARK 465 LEU B 2 REMARK 465 ALA B 3 REMARK 465 ASN B 4 REMARK 465 SER B 5 REMARK 465 ALA B 6 REMARK 465 SER B 7 REMARK 465 LYS B 483 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP B 317 CB - CG - OD2 ANGL. DEV. = 7.2 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 HIS A 70 16.60 56.67 REMARK 500 LEU A 166 -66.72 -122.33 REMARK 500 ASP A 317 10.04 87.37 REMARK 500 ARG A 327 68.75 -160.21 REMARK 500 MET A 336 -8.30 -59.82 REMARK 500 SER A 378 -47.22 -139.26 REMARK 500 ASN A 386 39.33 71.84 REMARK 500 ASN A 429 -5.46 73.33 REMARK 500 HIS B 70 18.82 56.79 REMARK 500 THR B 162 -166.39 -126.62 REMARK 500 LEU B 166 -59.79 -127.82 REMARK 500 ASP B 317 13.24 88.41 REMARK 500 ARG B 327 68.66 -160.13 REMARK 500 SER B 378 -46.45 -137.09 REMARK 500 ASN B 386 39.06 75.81 REMARK 500 ASN B 429 -3.59 74.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1483 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 179 NE2 REMARK 620 2 ASP A 183 OD2 92.8 REMARK 620 3 HOH A2001 O 107.1 127.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1484 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 282 ND1 REMARK 620 2 HIS A 290 NE2 101.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1483 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 179 NE2 REMARK 620 2 ASP B 183 OD2 105.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1484 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 282 ND1 REMARK 620 2 HIS B 290 NE2 104.2 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1483 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1484 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1483 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1484 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4B90 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF WT HUMAN CRMP-5 REMARK 900 RELATED ID: 4B91 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF TRUNCATED HUMAN CRMP-5 DBREF 4B92 A 1 483 UNP Q9BPU6 DPYL5_HUMAN 1 483 DBREF 4B92 B 1 483 UNP Q9BPU6 DPYL5_HUMAN 1 483 SEQADV 4B92 SER A 0 UNP Q9BPU6 EXPRESSION TAG SEQADV 4B92 SER B 0 UNP Q9BPU6 EXPRESSION TAG SEQRES 1 A 484 SER MET LEU ALA ASN SER ALA SER VAL ARG ILE LEU ILE SEQRES 2 A 484 LYS GLY GLY LYS VAL VAL ASN ASP ASP CYS THR HIS GLU SEQRES 3 A 484 ALA ASP VAL TYR ILE GLU ASN GLY ILE ILE GLN GLN VAL SEQRES 4 A 484 GLY ARG GLU LEU MET ILE PRO GLY GLY ALA LYS VAL ILE SEQRES 5 A 484 ASP ALA THR GLY LYS LEU VAL ILE PRO GLY GLY ILE ASP SEQRES 6 A 484 THR SER THR HIS PHE HIS GLN THR PHE MET ASN ALA THR SEQRES 7 A 484 CYS VAL ASP ASP PHE TYR HIS GLY THR LYS ALA ALA LEU SEQRES 8 A 484 VAL GLY GLY THR THR MET ILE ILE GLY HIS VAL LEU PRO SEQRES 9 A 484 ASP LYS GLU THR SER LEU VAL ASP ALA TYR GLU LYS CYS SEQRES 10 A 484 ARG GLY LEU ALA ASP PRO LYS VAL CYS CYS ASP TYR ALA SEQRES 11 A 484 LEU HIS VAL GLY ILE THR TRP TRP ALA PRO LYS VAL LYS SEQRES 12 A 484 ALA GLU MET GLU THR LEU VAL ARG GLU LYS GLY VAL ASN SEQRES 13 A 484 SER PHE GLN MET PHE MET THR TYR LYS ASP LEU TYR MET SEQRES 14 A 484 LEU ARG ASP SER GLU LEU TYR GLN VAL LEU HIS ALA CYS SEQRES 15 A 484 LYS ASP ILE GLY ALA ILE ALA ARG VAL HIS ALA GLU ASN SEQRES 16 A 484 GLY GLU LEU VAL ALA GLU GLY ALA LYS GLU ALA LEU ASP SEQRES 17 A 484 LEU GLY ILE THR GLY PRO GLU GLY ILE GLU ILE SER ARG SEQRES 18 A 484 PRO GLU GLU LEU GLU ALA GLU ALA THR HIS ARG VAL ILE SEQRES 19 A 484 THR ILE ALA ASN ARG THR HIS CYS PRO ILE TYR LEU VAL SEQRES 20 A 484 ASN VAL SER SER ILE SER ALA GLY ASP VAL ILE ALA ALA SEQRES 21 A 484 ALA LYS MET GLN GLY LYS VAL VAL LEU ALA GLU THR THR SEQRES 22 A 484 THR ALA HIS ALA THR LEU THR GLY LEU HIS TYR TYR HIS SEQRES 23 A 484 GLN ASP TRP SER HIS ALA ALA ALA TYR VAL THR VAL PRO SEQRES 24 A 484 PRO LEU ARG LEU ASP THR ASN THR SER THR TYR LEU MET SEQRES 25 A 484 SER LEU LEU ALA ASN ASP THR LEU ASN ILE VAL ALA SER SEQRES 26 A 484 ASP HIS ARG PRO PHE THR THR LYS GLN LYS ALA MET GLY SEQRES 27 A 484 LYS GLU ASP PHE THR LYS ILE PRO HIS GLY VAL SER GLY SEQRES 28 A 484 VAL GLN ASP ARG MET SER VAL ILE TRP GLU ARG GLY VAL SEQRES 29 A 484 VAL GLY GLY LYS MET ASP GLU ASN ARG PHE VAL ALA VAL SEQRES 30 A 484 THR SER SER ASN ALA ALA LYS LEU LEU ASN LEU TYR PRO SEQRES 31 A 484 ARG LYS GLY ARG ILE ILE PRO GLY ALA ASP ALA ASP VAL SEQRES 32 A 484 VAL VAL TRP ASP PRO GLU ALA THR LYS THR ILE SER ALA SEQRES 33 A 484 SER THR GLN VAL GLN GLY GLY ASP PHE ASN LEU TYR GLU SEQRES 34 A 484 ASN MET ARG CYS HIS GLY VAL PRO LEU VAL THR ILE SER SEQRES 35 A 484 ARG GLY ARG VAL VAL TYR GLU ASN GLY VAL PHE MET CYS SEQRES 36 A 484 ALA GLU GLY THR GLY LYS PHE CYS PRO LEU ARG SER PHE SEQRES 37 A 484 PRO ASP THR VAL TYR LYS LYS LEU VAL GLN ARG GLU LYS SEQRES 38 A 484 THR LEU LYS SEQRES 1 B 484 SER MET LEU ALA ASN SER ALA SER VAL ARG ILE LEU ILE SEQRES 2 B 484 LYS GLY GLY LYS VAL VAL ASN ASP ASP CYS THR HIS GLU SEQRES 3 B 484 ALA ASP VAL TYR ILE GLU ASN GLY ILE ILE GLN GLN VAL SEQRES 4 B 484 GLY ARG GLU LEU MET ILE PRO GLY GLY ALA LYS VAL ILE SEQRES 5 B 484 ASP ALA THR GLY LYS LEU VAL ILE PRO GLY GLY ILE ASP SEQRES 6 B 484 THR SER THR HIS PHE HIS GLN THR PHE MET ASN ALA THR SEQRES 7 B 484 CYS VAL ASP ASP PHE TYR HIS GLY THR LYS ALA ALA LEU SEQRES 8 B 484 VAL GLY GLY THR THR MET ILE ILE GLY HIS VAL LEU PRO SEQRES 9 B 484 ASP LYS GLU THR SER LEU VAL ASP ALA TYR GLU LYS CYS SEQRES 10 B 484 ARG GLY LEU ALA ASP PRO LYS VAL CYS CYS ASP TYR ALA SEQRES 11 B 484 LEU HIS VAL GLY ILE THR TRP TRP ALA PRO LYS VAL LYS SEQRES 12 B 484 ALA GLU MET GLU THR LEU VAL ARG GLU LYS GLY VAL ASN SEQRES 13 B 484 SER PHE GLN MET PHE MET THR TYR LYS ASP LEU TYR MET SEQRES 14 B 484 LEU ARG ASP SER GLU LEU TYR GLN VAL LEU HIS ALA CYS SEQRES 15 B 484 LYS ASP ILE GLY ALA ILE ALA ARG VAL HIS ALA GLU ASN SEQRES 16 B 484 GLY GLU LEU VAL ALA GLU GLY ALA LYS GLU ALA LEU ASP SEQRES 17 B 484 LEU GLY ILE THR GLY PRO GLU GLY ILE GLU ILE SER ARG SEQRES 18 B 484 PRO GLU GLU LEU GLU ALA GLU ALA THR HIS ARG VAL ILE SEQRES 19 B 484 THR ILE ALA ASN ARG THR HIS CYS PRO ILE TYR LEU VAL SEQRES 20 B 484 ASN VAL SER SER ILE SER ALA GLY ASP VAL ILE ALA ALA SEQRES 21 B 484 ALA LYS MET GLN GLY LYS VAL VAL LEU ALA GLU THR THR SEQRES 22 B 484 THR ALA HIS ALA THR LEU THR GLY LEU HIS TYR TYR HIS SEQRES 23 B 484 GLN ASP TRP SER HIS ALA ALA ALA TYR VAL THR VAL PRO SEQRES 24 B 484 PRO LEU ARG LEU ASP THR ASN THR SER THR TYR LEU MET SEQRES 25 B 484 SER LEU LEU ALA ASN ASP THR LEU ASN ILE VAL ALA SER SEQRES 26 B 484 ASP HIS ARG PRO PHE THR THR LYS GLN LYS ALA MET GLY SEQRES 27 B 484 LYS GLU ASP PHE THR LYS ILE PRO HIS GLY VAL SER GLY SEQRES 28 B 484 VAL GLN ASP ARG MET SER VAL ILE TRP GLU ARG GLY VAL SEQRES 29 B 484 VAL GLY GLY LYS MET ASP GLU ASN ARG PHE VAL ALA VAL SEQRES 30 B 484 THR SER SER ASN ALA ALA LYS LEU LEU ASN LEU TYR PRO SEQRES 31 B 484 ARG LYS GLY ARG ILE ILE PRO GLY ALA ASP ALA ASP VAL SEQRES 32 B 484 VAL VAL TRP ASP PRO GLU ALA THR LYS THR ILE SER ALA SEQRES 33 B 484 SER THR GLN VAL GLN GLY GLY ASP PHE ASN LEU TYR GLU SEQRES 34 B 484 ASN MET ARG CYS HIS GLY VAL PRO LEU VAL THR ILE SER SEQRES 35 B 484 ARG GLY ARG VAL VAL TYR GLU ASN GLY VAL PHE MET CYS SEQRES 36 B 484 ALA GLU GLY THR GLY LYS PHE CYS PRO LEU ARG SER PHE SEQRES 37 B 484 PRO ASP THR VAL TYR LYS LYS LEU VAL GLN ARG GLU LYS SEQRES 38 B 484 THR LEU LYS HET ZN A1483 1 HET ZN A1484 1 HET ZN B1483 1 HET ZN B1484 1 HETNAM ZN ZINC ION FORMUL 3 ZN 4(ZN 2+) FORMUL 7 HOH *3(H2 O) HELIX 1 1 ASP A 81 GLY A 92 1 12 HELIX 2 2 SER A 108 ASP A 121 1 14 HELIX 3 3 ALA A 138 LYS A 152 1 15 HELIX 4 4 ARG A 170 GLY A 185 1 16 HELIX 5 5 ASN A 194 LEU A 208 1 15 HELIX 6 6 GLU A 214 SER A 219 1 6 HELIX 7 7 GLU A 222 HIS A 240 1 19 HELIX 8 8 SER A 250 GLN A 263 1 14 HELIX 9 9 THR A 273 LEU A 278 1 6 HELIX 10 10 THR A 279 HIS A 285 5 7 HELIX 11 11 ASP A 287 TYR A 294 1 8 HELIX 12 12 ASN A 305 ASP A 317 1 13 HELIX 13 13 THR A 330 ALA A 335 1 6 HELIX 14 14 MET A 336 LYS A 338 5 3 HELIX 15 15 ASP A 340 ILE A 344 5 5 HELIX 16 16 ASP A 353 VAL A 363 1 11 HELIX 17 17 ASP A 369 SER A 378 1 10 HELIX 18 18 SER A 378 LEU A 385 1 8 HELIX 19 19 SER A 414 GLN A 418 5 5 HELIX 20 20 PRO A 468 LYS A 480 1 13 HELIX 21 21 ASP B 81 GLY B 92 1 12 HELIX 22 22 SER B 108 ASP B 121 1 14 HELIX 23 23 ALA B 138 LYS B 152 1 15 HELIX 24 24 ARG B 170 GLY B 185 1 16 HELIX 25 25 ASN B 194 LEU B 208 1 15 HELIX 26 26 GLU B 214 SER B 219 1 6 HELIX 27 27 GLU B 222 HIS B 240 1 19 HELIX 28 28 SER B 250 GLN B 263 1 14 HELIX 29 29 THR B 273 LEU B 278 1 6 HELIX 30 30 THR B 279 HIS B 285 5 7 HELIX 31 31 ASP B 287 TYR B 294 1 8 HELIX 32 32 ASN B 305 ASP B 317 1 13 HELIX 33 33 THR B 330 ALA B 335 1 6 HELIX 34 34 MET B 336 LYS B 338 5 3 HELIX 35 35 ASP B 340 ILE B 344 5 5 HELIX 36 36 ASP B 353 VAL B 363 1 11 HELIX 37 37 ASP B 369 SER B 378 1 10 HELIX 38 38 SER B 378 LEU B 385 1 8 HELIX 39 39 SER B 414 GLN B 418 5 5 HELIX 40 40 PRO B 468 LEU B 482 1 15 SHEET 1 AA 4 ILE A 34 GLY A 39 0 SHEET 2 AA 4 ASP A 27 GLU A 31 -1 O ASP A 27 N GLY A 39 SHEET 3 AA 4 ARG A 9 LYS A 13 -1 O ILE A 10 N ILE A 30 SHEET 4 AA 4 LYS A 49 ASP A 52 1 O LYS A 49 N LEU A 11 SHEET 1 AB 7 THR A 23 GLU A 25 0 SHEET 2 AB 7 LYS A 16 VAL A 18 -1 O VAL A 17 N HIS A 24 SHEET 3 AB 7 LEU A 57 PRO A 60 1 O VAL A 58 N VAL A 18 SHEET 4 AB 7 VAL A 402 THR A 412 -1 O VAL A 403 N ILE A 59 SHEET 5 AB 7 ARG A 431 SER A 441 -1 O CYS A 432 N LYS A 411 SHEET 6 AB 7 ARG A 444 GLU A 448 -1 O ARG A 444 N SER A 441 SHEET 7 AB 7 VAL A 451 PHE A 452 -1 O VAL A 451 N GLU A 448 SHEET 1 AC 8 GLY A 62 THR A 67 0 SHEET 2 AC 8 THR A 94 VAL A 101 1 N THR A 95 O GLY A 62 SHEET 3 AC 8 ASP A 127 GLY A 133 1 O ASP A 127 N ILE A 97 SHEET 4 AC 8 SER A 156 PHE A 160 1 O SER A 156 N VAL A 132 SHEET 5 AC 8 ILE A 187 HIS A 191 1 O ILE A 187 N PHE A 157 SHEET 6 AC 8 ILE A 243 LEU A 245 1 O TYR A 244 N VAL A 190 SHEET 7 AC 8 VAL A 267 THR A 272 1 O LEU A 268 N LEU A 245 SHEET 8 AC 8 ILE A 321 ALA A 323 1 O ILE A 321 N THR A 271 SHEET 1 AD 2 THR A 72 PHE A 73 0 SHEET 2 AD 2 ALA A 76 THR A 77 -1 O ALA A 76 N PHE A 73 SHEET 1 BA 4 ILE B 34 GLY B 39 0 SHEET 2 BA 4 ASP B 27 GLU B 31 -1 O ASP B 27 N GLY B 39 SHEET 3 BA 4 ARG B 9 LYS B 13 -1 O ILE B 10 N ILE B 30 SHEET 4 BA 4 LYS B 49 ASP B 52 1 O LYS B 49 N LEU B 11 SHEET 1 BB 7 THR B 23 GLU B 25 0 SHEET 2 BB 7 LYS B 16 VAL B 18 -1 O VAL B 17 N HIS B 24 SHEET 3 BB 7 LEU B 57 PRO B 60 1 O VAL B 58 N VAL B 18 SHEET 4 BB 7 VAL B 402 ASP B 406 -1 O VAL B 403 N ILE B 59 SHEET 5 BB 7 VAL B 435 SER B 441 -1 O VAL B 435 N ASP B 406 SHEET 6 BB 7 ARG B 444 GLU B 448 -1 O ARG B 444 N SER B 441 SHEET 7 BB 7 VAL B 451 PHE B 452 -1 O VAL B 451 N GLU B 448 SHEET 1 BC 8 GLY B 62 THR B 67 0 SHEET 2 BC 8 THR B 94 VAL B 101 1 N THR B 95 O GLY B 62 SHEET 3 BC 8 ASP B 127 GLY B 133 1 O ASP B 127 N ILE B 97 SHEET 4 BC 8 SER B 156 PHE B 160 1 O SER B 156 N VAL B 132 SHEET 5 BC 8 ILE B 187 HIS B 191 1 O ILE B 187 N PHE B 157 SHEET 6 BC 8 ILE B 243 LEU B 245 1 O TYR B 244 N VAL B 190 SHEET 7 BC 8 VAL B 267 THR B 272 1 O LEU B 268 N LEU B 245 SHEET 8 BC 8 ILE B 321 ALA B 323 1 O ILE B 321 N THR B 271 SHEET 1 BD 2 THR B 72 PHE B 73 0 SHEET 2 BD 2 ALA B 76 THR B 77 -1 O ALA B 76 N PHE B 73 LINK NE2 HIS A 179 ZN ZN A1483 1555 1555 2.18 LINK OD2 ASP A 183 ZN ZN A1483 1555 1555 2.04 LINK ND1 HIS A 282 ZN ZN A1484 1555 1555 2.19 LINK NE2 HIS A 290 ZN ZN A1484 1555 1555 2.19 LINK ZN ZN A1483 O HOH A2001 1555 1555 2.50 LINK NE2 HIS B 179 ZN ZN B1483 1555 1555 2.17 LINK OD2 ASP B 183 ZN ZN B1483 1555 1555 2.03 LINK ND1 HIS B 282 ZN ZN B1484 1555 1555 2.16 LINK NE2 HIS B 290 ZN ZN B1484 1555 1555 2.15 CISPEP 1 VAL A 297 PRO A 298 0 -5.88 CISPEP 2 TYR A 388 PRO A 389 0 1.46 CISPEP 3 VAL B 297 PRO B 298 0 -7.52 CISPEP 4 TYR B 388 PRO B 389 0 1.24 SITE 1 AC1 3 HIS A 179 ASP A 183 HOH A2001 SITE 1 AC2 4 HIS A 282 HIS A 285 HIS A 290 HOH A2002 SITE 1 AC3 2 HIS B 179 ASP B 183 SITE 1 AC4 4 HIS B 282 HIS B 285 HIS B 290 HOH B2001 CRYST1 89.500 89.500 246.460 90.00 90.00 90.00 P 41 21 2 16 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 0.011173 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011173 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004057 0.00000