HEADER SIGNALING PROTEIN 15-OCT-14 4V31 TITLE CEREBLON ISOFORM 4 FROM MAGNETOSPIRILLUM GRYPHISWALDENSE IN TITLE 2 COMPLEX WITH DEOXYURIDINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CEREBLON ISOFORM 4; COMPND 3 CHAIN: A, B, C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MAGNETOSPIRILLUM GRYPHISWALDENSE; SOURCE 3 ORGANISM_TAXID: 431944; SOURCE 4 STRAIN: MSR-1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SIGNALING PROTEIN, TERATOGENICITY, AROMATIC CAGE EXPDTA X-RAY DIFFRACTION AUTHOR M.D.HARTMANN,A.N.LUPAS,B.HERNANDEZ ALVAREZ REVDAT 1 17-DEC-14 4V31 0 JRNL AUTH M.D.HARTMANN,I.BOICHENKO,M.COLES,F.ZANINI,A.N.LUPAS, JRNL AUTH 2 B.HERNANDEZ ALVAREZ JRNL TITL THALIDOMIDE MIMICS URIDINE BINDING TO AN AROMATIC CAGE IN JRNL TITL 2 CEREBLON. JRNL REF J.STRUCT.BIOL. V. 188 225 2014 JRNL REFN ISSN 1047-8477 JRNL PMID 25448889 JRNL DOI 10.1016/J.JSB.2014.10.010 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU, REMARK 3 STEINER,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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.41 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 99.59 REMARK 3 NUMBER OF REFLECTIONS : 27173 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) : 0.16656 REMARK 3 R VALUE (WORKING SET) : 0.16386 REMARK 3 FREE R VALUE : 0.21855 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0 REMARK 3 FREE R VALUE TEST SET COUNT : 1434 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) : 1.799 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.846 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1930 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.86 REMARK 3 BIN R VALUE (WORKING SET) : 0.227 REMARK 3 BIN FREE R VALUE SET COUNT : 105 REMARK 3 BIN FREE R VALUE : 0.285 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2519 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 64 REMARK 3 SOLVENT ATOMS : 164 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.222 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.50 REMARK 3 B22 (A**2) : 2.14 REMARK 3 B33 (A**2) : -3.63 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.124 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.127 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.086 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.823 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.921 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2670 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2380 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3623 ; 1.868 ; 1.938 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5455 ; 0.896 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 324 ; 6.538 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 121 ;36.878 ;21.983 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 373 ;14.390 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;14.724 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 353 ; 0.129 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3070 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 718 ; 0.001 ; 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 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED 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 : 3 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 13 A 123 REMARK 3 ORIGIN FOR THE GROUP (A): 18.9764 17.4392 2.9664 REMARK 3 T TENSOR REMARK 3 T11: 0.0116 T22: 0.0322 REMARK 3 T33: 0.2757 T12: 0.0020 REMARK 3 T13: -0.0059 T23: -0.0126 REMARK 3 L TENSOR REMARK 3 L11: 1.7395 L22: 1.8064 REMARK 3 L33: 4.3188 L12: 0.0260 REMARK 3 L13: 1.1238 L23: 1.4221 REMARK 3 S TENSOR REMARK 3 S11: 0.0704 S12: 0.0424 S13: -0.1958 REMARK 3 S21: 0.0598 S22: -0.0310 S23: 0.0949 REMARK 3 S31: 0.2172 S32: -0.0459 S33: -0.0394 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 : B 19 B 123 REMARK 3 ORIGIN FOR THE GROUP (A): 32.0507 7.5624 23.7339 REMARK 3 T TENSOR REMARK 3 T11: 0.0322 T22: 0.0021 REMARK 3 T33: 0.2366 T12: -0.0038 REMARK 3 T13: 0.0103 T23: 0.0018 REMARK 3 L TENSOR REMARK 3 L11: 3.0425 L22: 2.1372 REMARK 3 L33: 2.7478 L12: -0.9659 REMARK 3 L13: 0.5822 L23: -0.7815 REMARK 3 S TENSOR REMARK 3 S11: 0.0342 S12: 0.0535 S13: -0.1119 REMARK 3 S21: -0.0552 S22: 0.0006 S23: 0.0387 REMARK 3 S31: 0.0021 S32: -0.0211 S33: -0.0348 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 : C 17 C 123 REMARK 3 ORIGIN FOR THE GROUP (A): 27.6899 -6.3595 -7.0703 REMARK 3 T TENSOR REMARK 3 T11: 0.1062 T22: 0.2214 REMARK 3 T33: 0.3664 T12: -0.0512 REMARK 3 T13: 0.0334 T23: -0.0144 REMARK 3 L TENSOR REMARK 3 L11: 3.9660 L22: 4.2515 REMARK 3 L33: 3.8096 L12: 1.2517 REMARK 3 L13: 1.1414 L23: 0.2993 REMARK 3 S TENSOR REMARK 3 S11: 0.0191 S12: -0.1331 S13: -0.0959 REMARK 3 S21: -0.0833 S22: -0.0179 S23: 0.4682 REMARK 3 S31: 0.3305 S32: -0.6794 S33: -0.0012 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 REMARK 3 RIDING POSITIONS. U VALUES WITH TLS ADDED REMARK 4 REMARK 4 4V31 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-OCT-14. REMARK 100 THE PDBE ID CODE IS EBI-61993. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-NOV-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL (PILATUS 6M) REMARK 200 DETECTOR MANUFACTURER : DECTRIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28709 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.80 REMARK 200 RESOLUTION RANGE LOW (A) : 37.40 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 2.87 REMARK 200 R MERGE (I) : 0.08 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.71 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.74 REMARK 200 R MERGE FOR SHELL (I) : 0.50 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.33 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.8 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CITRIC ACID PH 3.5, 25 REMARK 280 %(W/V) PEG 3350 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 28.40450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.18500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.99650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.18500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.40450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.99650 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 ALA A 0 REMARK 465 MET A 1 REMARK 465 PRO A 2 REMARK 465 LEU A 3 REMARK 465 ASP A 4 REMARK 465 ALA A 5 REMARK 465 GLY A 6 REMARK 465 GLY A 7 REMARK 465 GLN A 8 REMARK 465 ASN A 9 REMARK 465 SER A 10 REMARK 465 THR A 11 REMARK 465 GLN A 12 REMARK 465 ASP A 124 REMARK 465 ALA B 0 REMARK 465 MET B 1 REMARK 465 PRO B 2 REMARK 465 LEU B 3 REMARK 465 ASP B 4 REMARK 465 ALA B 5 REMARK 465 GLY B 6 REMARK 465 GLY B 7 REMARK 465 GLN B 8 REMARK 465 ASN B 9 REMARK 465 SER B 10 REMARK 465 THR B 11 REMARK 465 GLN B 12 REMARK 465 MET B 13 REMARK 465 VAL B 14 REMARK 465 LEU B 15 REMARK 465 ALA B 16 REMARK 465 PRO B 17 REMARK 465 GLY B 18 REMARK 465 ASP B 124 REMARK 465 ALA C 0 REMARK 465 MET C 1 REMARK 465 PRO C 2 REMARK 465 LEU C 3 REMARK 465 ASP C 4 REMARK 465 ALA C 5 REMARK 465 GLY C 6 REMARK 465 GLY C 7 REMARK 465 GLN C 8 REMARK 465 ASN C 9 REMARK 465 SER C 10 REMARK 465 THR C 11 REMARK 465 GLN C 12 REMARK 465 MET C 13 REMARK 465 VAL C 14 REMARK 465 LEU C 15 REMARK 465 ALA C 16 REMARK 465 ASP C 124 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 MET A 13 CG SD CE REMARK 470 ARG A 68 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 68 CD NE CZ NH1 NH2 REMARK 470 MET C 54 CG SD CE REMARK 470 LYS C 81 CG CD CE NZ REMARK 470 GLN C 106 CG CD OE1 NE2 REMARK 470 GLU C 120 CG CD OE1 OE2 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 84 CB - CG - OD2 ANGL. DEV. = -6.2 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 CYS A 27 -8.87 -144.09 REMARK 500 PHE A 77 14.79 57.43 REMARK 500 GLN A 92 -60.31 -94.01 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 A 150 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 90 SG REMARK 620 2 CYS A 27 SG 100.4 REMARK 620 3 CYS A 24 SG 108.9 112.3 REMARK 620 4 CYS A 93 SG 112.8 112.9 109.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 150 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 90 SG REMARK 620 2 CYS B 24 SG 111.3 REMARK 620 3 CYS B 27 SG 103.7 115.3 REMARK 620 4 CYS B 93 SG 112.0 102.6 112.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 150 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 24 SG REMARK 620 2 CYS C 90 SG 110.9 REMARK 620 3 CYS C 93 SG 105.1 113.6 REMARK 620 4 CYS C 27 SG 114.9 102.0 110.6 REMARK 620 N 1 2 3 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 150 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DUR A 151 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 150 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DUR B 151 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 150 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DUR C 151 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FLC B1124 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4V2Y RELATED DB: PDB REMARK 900 CEREBLON ISOFORM 4 FROM MAGNETOSPIRILLUM GRYPHISWALDENSE REMARK 900 IN COMPLEX WITH THALIDOMIDE REMARK 900 RELATED ID: 4V2Z RELATED DB: PDB REMARK 900 CEREBLON ISOFORM 4 FROM MAGNETOSPIRILLUM GRYPHISWALDENSE REMARK 900 IN COMPLEX WITH POMALIDOMIDE REMARK 900 RELATED ID: 4V30 RELATED DB: PDB REMARK 900 CEREBLON ISOFORM 4 FROM MAGNETOSPIRILLUM GRYPHISWALDENSE REMARK 900 IN COMPLEX WITH LENALIDOMIDE REMARK 900 RELATED ID: 4V32 RELATED DB: PDB REMARK 900 CEREBLON ISOFORM 4 FROM MAGNETOSPIRILLUM GRYPHISWALDENSE REMARK 900 IN COMPLEX WITH THALIDOMIDE, Y101F MUTANT DBREF 4V31 A 1 124 UNP A4TVL0 A4TVL0_9PROT 1 124 DBREF 4V31 B 1 124 UNP A4TVL0 A4TVL0_9PROT 1 124 DBREF 4V31 C 1 124 UNP A4TVL0 A4TVL0_9PROT 1 124 SEQADV 4V31 ALA A 0 UNP A4TVL0 EXPRESSION TAG SEQADV 4V31 ALA B 0 UNP A4TVL0 EXPRESSION TAG SEQADV 4V31 ALA C 0 UNP A4TVL0 EXPRESSION TAG SEQRES 1 A 125 ALA MET PRO LEU ASP ALA GLY GLY GLN ASN SER THR GLN SEQRES 2 A 125 MET VAL LEU ALA PRO GLY ALA SER ILE PHE ARG CYS ARG SEQRES 3 A 125 GLN CYS GLY GLN THR ILE SER ARG ARG ASP TRP LEU LEU SEQRES 4 A 125 PRO MET GLY GLY ASP HIS GLU HIS VAL VAL PHE ASN PRO SEQRES 5 A 125 ALA GLY MET ILE PHE ARG VAL TRP CYS PHE SER LEU ALA SEQRES 6 A 125 GLN GLY LEU ARG LEU ILE GLY ALA PRO SER GLY GLU PHE SEQRES 7 A 125 SER TRP PHE LYS GLY TYR ASP TRP THR ILE ALA LEU CYS SEQRES 8 A 125 GLY GLN CYS GLY SER HIS LEU GLY TRP HIS TYR GLU GLY SEQRES 9 A 125 GLY SER GLN PRO GLN THR PHE PHE GLY LEU ILE LYS ASP SEQRES 10 A 125 ARG LEU ALA GLU GLY PRO ALA ASP SEQRES 1 B 125 ALA MET PRO LEU ASP ALA GLY GLY GLN ASN SER THR GLN SEQRES 2 B 125 MET VAL LEU ALA PRO GLY ALA SER ILE PHE ARG CYS ARG SEQRES 3 B 125 GLN CYS GLY GLN THR ILE SER ARG ARG ASP TRP LEU LEU SEQRES 4 B 125 PRO MET GLY GLY ASP HIS GLU HIS VAL VAL PHE ASN PRO SEQRES 5 B 125 ALA GLY MET ILE PHE ARG VAL TRP CYS PHE SER LEU ALA SEQRES 6 B 125 GLN GLY LEU ARG LEU ILE GLY ALA PRO SER GLY GLU PHE SEQRES 7 B 125 SER TRP PHE LYS GLY TYR ASP TRP THR ILE ALA LEU CYS SEQRES 8 B 125 GLY GLN CYS GLY SER HIS LEU GLY TRP HIS TYR GLU GLY SEQRES 9 B 125 GLY SER GLN PRO GLN THR PHE PHE GLY LEU ILE LYS ASP SEQRES 10 B 125 ARG LEU ALA GLU GLY PRO ALA ASP SEQRES 1 C 125 ALA MET PRO LEU ASP ALA GLY GLY GLN ASN SER THR GLN SEQRES 2 C 125 MET VAL LEU ALA PRO GLY ALA SER ILE PHE ARG CYS ARG SEQRES 3 C 125 GLN CYS GLY GLN THR ILE SER ARG ARG ASP TRP LEU LEU SEQRES 4 C 125 PRO MET GLY GLY ASP HIS GLU HIS VAL VAL PHE ASN PRO SEQRES 5 C 125 ALA GLY MET ILE PHE ARG VAL TRP CYS PHE SER LEU ALA SEQRES 6 C 125 GLN GLY LEU ARG LEU ILE GLY ALA PRO SER GLY GLU PHE SEQRES 7 C 125 SER TRP PHE LYS GLY TYR ASP TRP THR ILE ALA LEU CYS SEQRES 8 C 125 GLY GLN CYS GLY SER HIS LEU GLY TRP HIS TYR GLU GLY SEQRES 9 C 125 GLY SER GLN PRO GLN THR PHE PHE GLY LEU ILE LYS ASP SEQRES 10 C 125 ARG LEU ALA GLU GLY PRO ALA ASP HET ZN A 150 1 HET DUR A 151 16 HET ZN B 150 1 HET DUR B 151 16 HET ZN C 150 1 HET DUR C 151 16 HET FLC B1124 13 HETNAM FLC CITRATE ANION HETNAM DUR 2'-DEOXYURIDINE HETNAM ZN ZINC ION FORMUL 2 FLC C6 H5 O7 3- FORMUL 3 DUR 3(C9 H12 N2 O5) FORMUL 4 ZN 3(ZN 2+) FORMUL 5 HOH *164(H2 O) HELIX 1 1 PRO B 39 ASP B 43 5 5 SHEET 1 AA 3 THR A 30 ARG A 33 0 SHEET 2 AA 3 ILE A 21 CYS A 24 -1 O PHE A 22 N ILE A 31 SHEET 3 AA 3 LEU A 118 GLY A 121 -1 O ALA A 119 N ARG A 23 SHEET 1 AB 6 GLU A 45 PHE A 49 0 SHEET 2 AB 6 ILE A 55 PHE A 61 -1 O PHE A 56 N VAL A 48 SHEET 3 AB 6 PHE A 110 ILE A 114 -1 O PHE A 111 N PHE A 61 SHEET 4 AB 6 HIS A 96 GLU A 102 -1 O LEU A 97 N ILE A 114 SHEET 5 AB 6 ASP A 84 CYS A 90 -1 O ASP A 84 N GLU A 102 SHEET 6 AB 6 LEU A 67 SER A 74 -1 O ARG A 68 N LEU A 89 SHEET 1 BA 3 THR B 30 ARG B 33 0 SHEET 2 BA 3 SER B 20 CYS B 24 -1 O PHE B 22 N ILE B 31 SHEET 3 BA 3 LEU B 118 PRO B 122 -1 O ALA B 119 N ARG B 23 SHEET 1 BB 6 GLU B 45 PHE B 49 0 SHEET 2 BB 6 ILE B 55 PHE B 61 -1 O PHE B 56 N VAL B 48 SHEET 3 BB 6 THR B 109 ILE B 114 -1 O PHE B 111 N PHE B 61 SHEET 4 BB 6 HIS B 96 GLU B 102 -1 O LEU B 97 N ILE B 114 SHEET 5 BB 6 ASP B 84 CYS B 90 -1 O ASP B 84 N GLU B 102 SHEET 6 BB 6 LEU B 67 SER B 74 -1 O ARG B 68 N LEU B 89 SHEET 1 CA 3 THR C 30 ARG C 33 0 SHEET 2 CA 3 ILE C 21 CYS C 24 -1 O PHE C 22 N ILE C 31 SHEET 3 CA 3 LEU C 118 GLY C 121 -1 O ALA C 119 N ARG C 23 SHEET 1 CB 6 GLU C 45 PHE C 49 0 SHEET 2 CB 6 ILE C 55 PHE C 61 -1 O PHE C 56 N VAL C 48 SHEET 3 CB 6 PHE C 110 ILE C 114 -1 O PHE C 111 N PHE C 61 SHEET 4 CB 6 HIS C 96 GLU C 102 -1 O LEU C 97 N ILE C 114 SHEET 5 CB 6 ASP C 84 CYS C 90 -1 O ASP C 84 N GLU C 102 SHEET 6 CB 6 LEU C 67 SER C 74 -1 O ARG C 68 N LEU C 89 LINK ZN ZN A 150 SG CYS A 90 1555 1555 2.37 LINK ZN ZN A 150 SG CYS A 27 1555 1555 2.32 LINK ZN ZN A 150 SG CYS A 24 1555 1555 2.31 LINK ZN ZN A 150 SG CYS A 93 1555 1555 2.33 LINK ZN ZN B 150 SG CYS B 90 1555 1555 2.32 LINK ZN ZN B 150 SG CYS B 24 1555 1555 2.33 LINK ZN ZN B 150 SG CYS B 27 1555 1555 2.32 LINK ZN ZN B 150 SG CYS B 93 1555 1555 2.33 LINK ZN ZN C 150 SG CYS C 90 1555 1555 2.33 LINK ZN ZN C 150 SG CYS C 93 1555 1555 2.30 LINK ZN ZN C 150 SG CYS C 27 1555 1555 2.27 LINK ZN ZN C 150 SG CYS C 24 1555 1555 2.34 CISPEP 1 GLN A 106 PRO A 107 0 5.84 CISPEP 2 GLN B 106 PRO B 107 0 -2.33 CISPEP 3 GLN C 106 PRO C 107 0 -13.67 SITE 1 AC1 4 CYS A 24 CYS A 27 CYS A 90 CYS A 93 SITE 1 AC2 10 PRO A 51 PHE A 77 SER A 78 TRP A 79 SITE 2 AC2 10 TRP A 85 TRP A 99 TYR A 101 HOH A2021 SITE 3 AC2 10 HOH A2022 HOH A2077 SITE 1 AC3 4 CYS B 24 CYS B 27 CYS B 90 CYS B 93 SITE 1 AC4 10 ASN B 50 PRO B 51 PHE B 77 SER B 78 SITE 2 AC4 10 TRP B 79 TRP B 85 TRP B 99 TYR B 101 SITE 3 AC4 10 HOH B2019 HOH B2052 SITE 1 AC5 4 CYS C 24 CYS C 27 CYS C 90 CYS C 93 SITE 1 AC6 8 ILE B 70 PRO C 51 PHE C 77 SER C 78 SITE 2 AC6 8 TRP C 79 TRP C 85 TRP C 99 TYR C 101 SITE 1 AC7 10 ARG A 57 GLN A 108 THR A 109 HOH A2062 SITE 2 AC7 10 HOH A2069 ASP B 43 HIS B 44 HOH B2015 SITE 3 AC7 10 HOH B2016 GLN C 26 CRYST1 56.809 59.993 88.370 90.00 90.00 90.00 P 21 21 21 12 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 0.017603 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016669 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011316 0.00000