HEADER TRANSFERASE 09-NOV-07 3BBB TITLE CRYSTAL STRUCTURE OF THE NM23-H2 TRANSCRIPTION FACTOR COMPLEX WITH TITLE 2 DINUCLEOTIDE D(AG) COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOSIDE DIPHOSPHATE KINASE B; COMPND 3 CHAIN: A, B, C, D, E, F; COMPND 4 SYNONYM: NDK B,NDP KINASE B,C-MYC PURINE-BINDING TRANSCRIPTION FACTOR COMPND 5 PUF,HISTIDINE PROTEIN KINASE NDKB,NM23-H2; COMPND 6 EC: 2.7.4.6,2.7.13.3; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*AP*G)-3'); COMPND 10 CHAIN: G, H, I, J; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: NME2, NM23B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PLASMID; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630 KEYWDS TRANSCRIPTION FACTOR, CANCER, NM23 GEN, HEXAMER, ACTIVATOR, ANTI- KEYWDS 2 ONCOGENE, ATP-BINDING, CELL CYCLE, DNA-BINDING, KINASE, MAGNESIUM, KEYWDS 3 METAL-BINDING, NUCLEOTIDE METABOLISM, NUCLEOTIDE-BINDING, NUCLEUS, KEYWDS 4 PHOSPHORYLATION, TRANSCRIPTION REGULATION, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.WEICHSEL,W.R.MONTFORT REVDAT 6 29-MAY-24 3BBB 1 COMPND SOURCE REMARK DBREF REVDAT 6 2 1 SEQRES LINK SITE ATOM REVDAT 5 30-AUG-23 3BBB 1 REMARK LINK REVDAT 4 04-AUG-10 3BBB 1 JRNL REVDAT 3 11-AUG-09 3BBB 1 JRNL REVDAT 2 24-FEB-09 3BBB 1 VERSN REVDAT 1 23-SEP-08 3BBB 0 JRNL AUTH T.S.DEXHEIMER,S.S.CAREY,S.ZUOHE,V.M.GOKHALE,X.HU,L.B.MURATA, JRNL AUTH 2 E.M.MAES,A.WEICHSEL,D.SUN,E.J.MEUILLET,W.R.MONTFORT, JRNL AUTH 3 L.H.HURLEY JRNL TITL NM23-H2 MAY PLAY AN INDIRECT ROLE IN TRANSCRIPTIONAL JRNL TITL 2 ACTIVATION OF C-MYC GENE EXPRESSION BUT DOES NOT CLEAVE THE JRNL TITL 3 NUCLEASE HYPERSENSITIVE ELEMENT III1. JRNL REF MOL.CANCER THER. V. 8 1363 2009 JRNL REFN ISSN 1535-7163 JRNL PMID 19435876 JRNL DOI 10.1158/1535-7163.MCT-08-1093 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.MORERA,M.L.LACOMBE,Y.XU,G.LEBRAS,J.JANIN REMARK 1 TITL X-RAY STRUCTURE OF HUMAN NUCLEOSIDE DIPHOSPHATE KINASE B REMARK 1 TITL 2 COMPLEXED WITH GDP AT 2 A RESOLUTION. REMARK 1 REF STRUCTURE V. 3 1307 1995 REMARK 1 REFN ISSN 0969-2126 REMARK 1 PMID 8747457 REMARK 1 DOI 10.1016/S0969-2126(01)00268-4 REMARK 2 REMARK 2 RESOLUTION. 1.30 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 183782 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) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 9678 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) : 1.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.33 REMARK 3 REFLECTION IN BIN (WORKING SET) : 13198 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.05 REMARK 3 BIN R VALUE (WORKING SET) : 0.2060 REMARK 3 BIN FREE R VALUE SET COUNT : 674 REMARK 3 BIN FREE R VALUE : 0.2580 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7218 REMARK 3 NUCLEIC ACID ATOMS : 126 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 641 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.16 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.11000 REMARK 3 B22 (A**2) : 0.21000 REMARK 3 B33 (A**2) : -0.32000 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): 0.063 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.062 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.039 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.020 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7703 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 5427 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10432 ; 1.885 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): 13194 ; 1.202 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 938 ; 6.384 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 352 ;32.612 ;23.523 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1380 ;13.714 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 56 ;21.777 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1104 ; 0.187 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8472 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1588 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1563 ; 0.227 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 5704 ; 0.215 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3718 ; 0.187 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 3972 ; 0.084 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 471 ; 0.157 ; 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): 8 ; 0.163 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 26 ; 0.210 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 18 ; 0.137 ; 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): 5925 ; 2.265 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1866 ; 1.237 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 7393 ; 2.699 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3756 ; 3.688 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3025 ; 4.791 ; 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): 9451 ; 2.399 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 638 ;10.771 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 7374 ; 5.741 ; 3.000 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 REMARK 4 REMARK 4 3BBB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-DEC-07. REMARK 100 THE DEPOSITION ID IS D_1000045311. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-BM-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 195789 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 27.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.42000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1NUE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 1500, 50 MM SODIUM CITRATE, 20 MM REMARK 280 MGCL2, 5 MM DTT, CRYSTALS SOAKED WITH 10 MM D(AG), PH 6.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 26.23300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 64.45500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 59.10950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 64.45500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.23300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 59.10950 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DECAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H, I, J 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 C 2 REMARK 465 ASN C 3 REMARK 465 LEU C 4 REMARK 465 ALA E 2 REMARK 465 ASN E 3 REMARK 465 LEU E 4 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 DA G 201 O5' C5' C4' O4' C3' C2' C1' REMARK 470 DA G 201 N9 C8 N7 C5 C6 N6 N1 REMARK 470 DA G 201 C2 N3 C4 REMARK 470 DA J 201 O5' C5' C4' O4' C3' C2' C1' REMARK 470 DA J 201 N9 C8 N7 C5 C6 N6 N1 REMARK 470 DA J 201 C2 N3 C4 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 GLU A 137 CB GLU A 137 CG -0.137 REMARK 500 TYR C 67 CB TYR C 67 CG 0.091 REMARK 500 GLU E 5 CB GLU E 5 CG -0.162 REMARK 500 GLU E 5 CD GLU E 5 OE2 -0.078 REMARK 500 TYR E 67 CB TYR E 67 CG 0.096 REMARK 500 GLU E 127 CG GLU E 127 CD 0.091 REMARK 500 DA J 201 O3' DG J 202 P -0.124 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 ARG A 27 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG B 6 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG B 88 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DG G 202 O4' - C1' - N9 ANGL. DEV. = 15.4 DEGREES REMARK 500 DG G 202 N3 - C4 - C5 ANGL. DEV. = -4.0 DEGREES REMARK 500 DG G 202 N3 - C4 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 DG G 202 C6 - C5 - N7 ANGL. DEV. = -4.2 DEGREES REMARK 500 DG G 202 C8 - N9 - C1' ANGL. DEV. = -11.9 DEGREES REMARK 500 DG G 202 C4 - N9 - C1' ANGL. DEV. = 13.8 DEGREES REMARK 500 DG I 202 O4' - C1' - C2' ANGL. DEV. = -4.8 DEGREES REMARK 500 DG I 202 O4' - C1' - N9 ANGL. DEV. = 5.0 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 ILE A 116 -23.08 56.93 REMARK 500 ILE B 116 -22.38 54.66 REMARK 500 ILE C 116 -24.78 63.23 REMARK 500 ILE D 116 -24.69 56.39 REMARK 500 ILE E 116 -24.56 59.53 REMARK 500 ILE F 116 -23.47 62.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH E 421 DISTANCE = 6.03 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NUE RELATED DB: PDB REMARK 900 THE SAME PROTEIN REMARK 900 RELATED ID: 3BBC RELATED DB: PDB REMARK 900 RELATED ID: 3BBF RELATED DB: PDB DBREF 3BBB A 2 152 UNP P22392 NDKB_HUMAN 2 152 DBREF 3BBB B 2 152 UNP P22392 NDKB_HUMAN 2 152 DBREF 3BBB C 2 152 UNP P22392 NDKB_HUMAN 2 152 DBREF 3BBB D 2 152 UNP P22392 NDKB_HUMAN 2 152 DBREF 3BBB E 2 152 UNP P22392 NDKB_HUMAN 2 152 DBREF 3BBB F 2 152 UNP P22392 NDKB_HUMAN 2 152 DBREF 3BBB G 201 202 PDB 3BBB 3BBB 201 202 DBREF 3BBB H 201 202 PDB 3BBB 3BBB 201 202 DBREF 3BBB I 201 202 PDB 3BBB 3BBB 201 202 DBREF 3BBB J 201 202 PDB 3BBB 3BBB 201 202 SEQRES 1 A 151 ALA ASN LEU GLU ARG THR PHE ILE ALA ILE LYS PRO ASP SEQRES 2 A 151 GLY VAL GLN ARG GLY LEU VAL GLY GLU ILE ILE LYS ARG SEQRES 3 A 151 PHE GLU GLN LYS GLY PHE ARG LEU VAL ALA MET LYS PHE SEQRES 4 A 151 LEU ARG ALA SER GLU GLU HIS LEU LYS GLN HIS TYR ILE SEQRES 5 A 151 ASP LEU LYS ASP ARG PRO PHE PHE PRO GLY LEU VAL LYS SEQRES 6 A 151 TYR MET ASN SER GLY PRO VAL VAL ALA MET VAL TRP GLU SEQRES 7 A 151 GLY LEU ASN VAL VAL LYS THR GLY ARG VAL MET LEU GLY SEQRES 8 A 151 GLU THR ASN PRO ALA ASP SER LYS PRO GLY THR ILE ARG SEQRES 9 A 151 GLY ASP PHE CYS ILE GLN VAL GLY ARG ASN ILE ILE HIS SEQRES 10 A 151 GLY SER ASP SER VAL LYS SER ALA GLU LYS GLU ILE SER SEQRES 11 A 151 LEU TRP PHE LYS PRO GLU GLU LEU VAL ASP TYR LYS SER SEQRES 12 A 151 CYS ALA HIS ASP TRP VAL TYR GLU SEQRES 1 B 151 ALA ASN LEU GLU ARG THR PHE ILE ALA ILE LYS PRO ASP SEQRES 2 B 151 GLY VAL GLN ARG GLY LEU VAL GLY GLU ILE ILE LYS ARG SEQRES 3 B 151 PHE GLU GLN LYS GLY PHE ARG LEU VAL ALA MET LYS PHE SEQRES 4 B 151 LEU ARG ALA SER GLU GLU HIS LEU LYS GLN HIS TYR ILE SEQRES 5 B 151 ASP LEU LYS ASP ARG PRO PHE PHE PRO GLY LEU VAL LYS SEQRES 6 B 151 TYR MET ASN SER GLY PRO VAL VAL ALA MET VAL TRP GLU SEQRES 7 B 151 GLY LEU ASN VAL VAL LYS THR GLY ARG VAL MET LEU GLY SEQRES 8 B 151 GLU THR ASN PRO ALA ASP SER LYS PRO GLY THR ILE ARG SEQRES 9 B 151 GLY ASP PHE CYS ILE GLN VAL GLY ARG ASN ILE ILE HIS SEQRES 10 B 151 GLY SER ASP SER VAL LYS SER ALA GLU LYS GLU ILE SER SEQRES 11 B 151 LEU TRP PHE LYS PRO GLU GLU LEU VAL ASP TYR LYS SER SEQRES 12 B 151 CYS ALA HIS ASP TRP VAL TYR GLU SEQRES 1 C 151 ALA ASN LEU GLU ARG THR PHE ILE ALA ILE LYS PRO ASP SEQRES 2 C 151 GLY VAL GLN ARG GLY LEU VAL GLY GLU ILE ILE LYS ARG SEQRES 3 C 151 PHE GLU GLN LYS GLY PHE ARG LEU VAL ALA MET LYS PHE SEQRES 4 C 151 LEU ARG ALA SER GLU GLU HIS LEU LYS GLN HIS TYR ILE SEQRES 5 C 151 ASP LEU LYS ASP ARG PRO PHE PHE PRO GLY LEU VAL LYS SEQRES 6 C 151 TYR MET ASN SER GLY PRO VAL VAL ALA MET VAL TRP GLU SEQRES 7 C 151 GLY LEU ASN VAL VAL LYS THR GLY ARG VAL MET LEU GLY SEQRES 8 C 151 GLU THR ASN PRO ALA ASP SER LYS PRO GLY THR ILE ARG SEQRES 9 C 151 GLY ASP PHE CYS ILE GLN VAL GLY ARG ASN ILE ILE HIS SEQRES 10 C 151 GLY SER ASP SER VAL LYS SER ALA GLU LYS GLU ILE SER SEQRES 11 C 151 LEU TRP PHE LYS PRO GLU GLU LEU VAL ASP TYR LYS SER SEQRES 12 C 151 CYS ALA HIS ASP TRP VAL TYR GLU SEQRES 1 D 151 ALA ASN LEU GLU ARG THR PHE ILE ALA ILE LYS PRO ASP SEQRES 2 D 151 GLY VAL GLN ARG GLY LEU VAL GLY GLU ILE ILE LYS ARG SEQRES 3 D 151 PHE GLU GLN LYS GLY PHE ARG LEU VAL ALA MET LYS PHE SEQRES 4 D 151 LEU ARG ALA SER GLU GLU HIS LEU LYS GLN HIS TYR ILE SEQRES 5 D 151 ASP LEU LYS ASP ARG PRO PHE PHE PRO GLY LEU VAL LYS SEQRES 6 D 151 TYR MET ASN SER GLY PRO VAL VAL ALA MET VAL TRP GLU SEQRES 7 D 151 GLY LEU ASN VAL VAL LYS THR GLY ARG VAL MET LEU GLY SEQRES 8 D 151 GLU THR ASN PRO ALA ASP SER LYS PRO GLY THR ILE ARG SEQRES 9 D 151 GLY ASP PHE CYS ILE GLN VAL GLY ARG ASN ILE ILE HIS SEQRES 10 D 151 GLY SER ASP SER VAL LYS SER ALA GLU LYS GLU ILE SER SEQRES 11 D 151 LEU TRP PHE LYS PRO GLU GLU LEU VAL ASP TYR LYS SER SEQRES 12 D 151 CYS ALA HIS ASP TRP VAL TYR GLU SEQRES 1 E 151 ALA ASN LEU GLU ARG THR PHE ILE ALA ILE LYS PRO ASP SEQRES 2 E 151 GLY VAL GLN ARG GLY LEU VAL GLY GLU ILE ILE LYS ARG SEQRES 3 E 151 PHE GLU GLN LYS GLY PHE ARG LEU VAL ALA MET LYS PHE SEQRES 4 E 151 LEU ARG ALA SER GLU GLU HIS LEU LYS GLN HIS TYR ILE SEQRES 5 E 151 ASP LEU LYS ASP ARG PRO PHE PHE PRO GLY LEU VAL LYS SEQRES 6 E 151 TYR MET ASN SER GLY PRO VAL VAL ALA MET VAL TRP GLU SEQRES 7 E 151 GLY LEU ASN VAL VAL LYS THR GLY ARG VAL MET LEU GLY SEQRES 8 E 151 GLU THR ASN PRO ALA ASP SER LYS PRO GLY THR ILE ARG SEQRES 9 E 151 GLY ASP PHE CYS ILE GLN VAL GLY ARG ASN ILE ILE HIS SEQRES 10 E 151 GLY SER ASP SER VAL LYS SER ALA GLU LYS GLU ILE SER SEQRES 11 E 151 LEU TRP PHE LYS PRO GLU GLU LEU VAL ASP TYR LYS SER SEQRES 12 E 151 CYS ALA HIS ASP TRP VAL TYR GLU SEQRES 1 F 151 ALA ASN LEU GLU ARG THR PHE ILE ALA ILE LYS PRO ASP SEQRES 2 F 151 GLY VAL GLN ARG GLY LEU VAL GLY GLU ILE ILE LYS ARG SEQRES 3 F 151 PHE GLU GLN LYS GLY PHE ARG LEU VAL ALA MET LYS PHE SEQRES 4 F 151 LEU ARG ALA SER GLU GLU HIS LEU LYS GLN HIS TYR ILE SEQRES 5 F 151 ASP LEU LYS ASP ARG PRO PHE PHE PRO GLY LEU VAL LYS SEQRES 6 F 151 TYR MET ASN SER GLY PRO VAL VAL ALA MET VAL TRP GLU SEQRES 7 F 151 GLY LEU ASN VAL VAL LYS THR GLY ARG VAL MET LEU GLY SEQRES 8 F 151 GLU THR ASN PRO ALA ASP SER LYS PRO GLY THR ILE ARG SEQRES 9 F 151 GLY ASP PHE CYS ILE GLN VAL GLY ARG ASN ILE ILE HIS SEQRES 10 F 151 GLY SER ASP SER VAL LYS SER ALA GLU LYS GLU ILE SER SEQRES 11 F 151 LEU TRP PHE LYS PRO GLU GLU LEU VAL ASP TYR LYS SER SEQRES 12 F 151 CYS ALA HIS ASP TRP VAL TYR GLU SEQRES 1 G 2 DA DG SEQRES 1 H 2 DA DG SEQRES 1 I 2 DA DG SEQRES 1 J 2 DA DG FORMUL 11 HOH *641(H2 O) HELIX 1 1 LYS A 12 ARG A 18 1 7 HELIX 2 2 LEU A 20 GLY A 32 1 13 HELIX 3 3 SER A 44 TYR A 52 1 9 HELIX 4 4 ILE A 53 LYS A 56 5 4 HELIX 5 5 PHE A 60 ASN A 69 1 10 HELIX 6 6 ASN A 82 GLY A 92 1 11 HELIX 7 7 ASN A 95 SER A 99 5 5 HELIX 8 8 THR A 103 CYS A 109 1 7 HELIX 9 9 GLN A 111 ASN A 115 5 5 HELIX 10 10 SER A 122 PHE A 134 1 13 HELIX 11 11 LYS A 135 LEU A 139 5 5 HELIX 12 12 ALA A 146 TYR A 151 1 6 HELIX 13 13 LYS B 12 ARG B 18 1 7 HELIX 14 14 LEU B 20 GLY B 32 1 13 HELIX 15 15 SER B 44 TYR B 52 1 9 HELIX 16 16 ILE B 53 LYS B 56 5 4 HELIX 17 17 PHE B 60 SER B 70 1 11 HELIX 18 18 ASN B 82 GLY B 92 1 11 HELIX 19 19 ASN B 95 SER B 99 5 5 HELIX 20 20 THR B 103 CYS B 109 1 7 HELIX 21 21 GLN B 111 ASN B 115 5 5 HELIX 22 22 SER B 122 PHE B 134 1 13 HELIX 23 23 LYS B 135 LEU B 139 5 5 HELIX 24 24 ALA B 146 TYR B 151 1 6 HELIX 25 25 LYS C 12 ARG C 18 1 7 HELIX 26 26 LEU C 20 GLY C 32 1 13 HELIX 27 27 SER C 44 TYR C 52 1 9 HELIX 28 28 ILE C 53 LYS C 56 5 4 HELIX 29 29 PHE C 60 ASN C 69 1 10 HELIX 30 30 ASN C 82 GLY C 92 1 11 HELIX 31 31 ASN C 95 SER C 99 5 5 HELIX 32 32 THR C 103 CYS C 109 1 7 HELIX 33 33 GLN C 111 ASN C 115 5 5 HELIX 34 34 SER C 122 PHE C 134 1 13 HELIX 35 35 LYS C 135 LEU C 139 5 5 HELIX 36 36 ALA C 146 TYR C 151 1 6 HELIX 37 37 LYS D 12 ARG D 18 1 7 HELIX 38 38 LEU D 20 GLY D 32 1 13 HELIX 39 39 SER D 44 TYR D 52 1 9 HELIX 40 40 ILE D 53 LYS D 56 5 4 HELIX 41 41 PHE D 60 ASN D 69 1 10 HELIX 42 42 ASN D 82 GLY D 92 1 11 HELIX 43 43 ASN D 95 SER D 99 5 5 HELIX 44 44 THR D 103 CYS D 109 1 7 HELIX 45 45 GLN D 111 ASN D 115 5 5 HELIX 46 46 SER D 122 PHE D 134 1 13 HELIX 47 47 LYS D 135 LEU D 139 5 5 HELIX 48 48 ALA D 146 TYR D 151 1 6 HELIX 49 49 LYS E 12 ARG E 18 1 7 HELIX 50 50 LEU E 20 GLY E 32 1 13 HELIX 51 51 SER E 44 TYR E 52 1 9 HELIX 52 52 ILE E 53 LYS E 56 5 4 HELIX 53 53 PHE E 60 ASN E 69 1 10 HELIX 54 54 ASN E 82 GLY E 92 1 11 HELIX 55 55 ASN E 95 SER E 99 5 5 HELIX 56 56 THR E 103 CYS E 109 1 7 HELIX 57 57 GLN E 111 ASN E 115 5 5 HELIX 58 58 SER E 122 PHE E 134 1 13 HELIX 59 59 LYS E 135 LEU E 139 5 5 HELIX 60 60 ALA E 146 TYR E 151 1 6 HELIX 61 61 LYS F 12 ARG F 18 1 7 HELIX 62 62 LEU F 20 GLY F 32 1 13 HELIX 63 63 SER F 44 TYR F 52 1 9 HELIX 64 64 ILE F 53 LYS F 56 5 4 HELIX 65 65 PHE F 60 ASN F 69 1 10 HELIX 66 66 ASN F 82 GLY F 92 1 11 HELIX 67 67 ASN F 95 SER F 99 5 5 HELIX 68 68 THR F 103 CYS F 109 1 7 HELIX 69 69 GLN F 111 ASN F 115 5 5 HELIX 70 70 SER F 122 PHE F 134 1 13 HELIX 71 71 LYS F 135 LEU F 139 5 5 HELIX 72 72 ALA F 146 TYR F 151 1 6 SHEET 1 A 4 ARG A 34 LEU A 41 0 SHEET 2 A 4 VAL A 73 GLU A 79 -1 O VAL A 77 N VAL A 36 SHEET 3 A 4 ARG A 6 ILE A 11 -1 N ILE A 11 O VAL A 74 SHEET 4 A 4 ILE A 117 GLY A 119 -1 O HIS A 118 N ALA A 10 SHEET 1 B 4 ARG B 34 LEU B 41 0 SHEET 2 B 4 VAL B 73 GLU B 79 -1 O VAL B 73 N LEU B 41 SHEET 3 B 4 ARG B 6 ILE B 11 -1 N ILE B 11 O VAL B 74 SHEET 4 B 4 ILE B 117 GLY B 119 -1 O HIS B 118 N ALA B 10 SHEET 1 C 4 ARG C 34 LEU C 41 0 SHEET 2 C 4 VAL C 73 GLU C 79 -1 O VAL C 73 N LEU C 41 SHEET 3 C 4 ARG C 6 ILE C 11 -1 N ILE C 11 O VAL C 74 SHEET 4 C 4 ILE C 117 GLY C 119 -1 O HIS C 118 N ALA C 10 SHEET 1 D 4 ARG D 34 LEU D 41 0 SHEET 2 D 4 VAL D 73 GLU D 79 -1 O VAL D 77 N VAL D 36 SHEET 3 D 4 ARG D 6 ILE D 11 -1 N ILE D 11 O VAL D 74 SHEET 4 D 4 ILE D 117 GLY D 119 -1 O HIS D 118 N ALA D 10 SHEET 1 E 4 ARG E 34 LEU E 41 0 SHEET 2 E 4 VAL E 73 GLU E 79 -1 O VAL E 77 N VAL E 36 SHEET 3 E 4 ARG E 6 ILE E 11 -1 N ILE E 11 O VAL E 74 SHEET 4 E 4 ILE E 117 GLY E 119 -1 O HIS E 118 N ALA E 10 SHEET 1 F 4 ARG F 34 LEU F 41 0 SHEET 2 F 4 VAL F 73 GLU F 79 -1 O VAL F 77 N VAL F 36 SHEET 3 F 4 ARG F 6 ILE F 11 -1 N ILE F 11 O VAL F 74 SHEET 4 F 4 ILE F 117 GLY F 119 -1 O HIS F 118 N ALA F 10 CRYST1 52.466 118.219 128.910 90.00 90.00 90.00 P 21 21 21 24 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 0.019060 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008459 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007757 0.00000