PDB Short entry for 2XMR HEADER SIGNALING PROTEIN 29-JUL-10 2XMR TITLE CRYSTAL STRUCTURE OF HUMAN NDRG2 PROTEIN PROVIDES INSIGHT INTO ITS TITLE 2 ROLE AS A TUMOR SUPPRESSOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN NDRG2; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: ALPHA-BETA HYDROLASE DOMAIN, RESIDUES 24-304; COMPND 5 SYNONYM: NDRG2; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: 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: 562 KEYWDS SIGNALING PROTEIN, NDRG FAMILY EXPDTA X-RAY DIFFRACTION AUTHOR J.HWANG,Y.KIM,H.LEE,M.H.KIM REVDAT 4 20-DEC-23 2XMR 1 REMARK LINK REVDAT 3 31-AUG-11 2XMR 1 JRNL REMARK VERSN REVDAT 2 02-FEB-11 2XMR 1 JRNL REVDAT 1 19-JAN-11 2XMR 0 JRNL AUTH J.HWANG,Y.KIM,H.B.KANG,L.JAROSZEWSKI,A.DEACON,H.LEE, JRNL AUTH 2 W.C.CHOI,K.J.KIM,C.H.KIM,B.S.KANG,J.O.LEE,T.K.OH,J.W.KIM, JRNL AUTH 3 I.A.WILSON,M.H.KIM JRNL TITL CRYSTAL STRUCTURE OF HUMAN NDRG2 PROTEIN PROVIDES INSIGHT JRNL TITL 2 INTO ITS ROLE AS A TUMOR SUPPRESSOR. JRNL REF J.BIOL.CHEM. V. 286 12450 2011 JRNL REFN ISSN 0021-9258 JRNL PMID 21247902 JRNL DOI 10.1074/JBC.M110.170803 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 60071 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) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3217 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.06 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4075 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.87 REMARK 3 BIN R VALUE (WORKING SET) : 0.2610 REMARK 3 BIN FREE R VALUE SET COUNT : 219 REMARK 3 BIN FREE R VALUE : 0.3570 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6591 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 399 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 0.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.61 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.45000 REMARK 3 B22 (A**2) : -0.10000 REMARK 3 B33 (A**2) : 0.55000 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): 0.174 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.164 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.126 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.335 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.930 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6801 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9263 ; 1.342 ; 1.962 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 842 ; 8.966 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 317 ;36.103 ;24.921 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1064 ;15.297 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;18.423 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1008 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5291 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3013 ; 0.205 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4656 ; 0.310 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 398 ; 0.154 ; 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): 64 ; 0.206 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.276 ; 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): 4318 ; 0.760 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6812 ; 1.245 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2819 ; 1.845 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2451 ; 2.900 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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. REMARK 4 REMARK 4 2XMR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-JUL-10. REMARK 100 THE DEPOSITION ID IS D_1290044856. 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 : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 6C1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.23985 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 63329 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.14000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.2700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.44000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.830 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 2QMQ REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG 8000, 0.2 M CALCIUM ACETATE, REMARK 280 0.1 M MES (PH 6.8 TO 7.1) 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 43.11600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.45350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.02450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.45350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 43.11600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.02450 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, LYS 45 TO ALA REMARK 400 ENGINEERED RESIDUE IN CHAIN A, LYS 47 TO ALA REMARK 400 ENGINEERED RESIDUE IN CHAIN B, LYS 45 TO ALA REMARK 400 ENGINEERED RESIDUE IN CHAIN B, LYS 47 TO ALA REMARK 400 ENGINEERED RESIDUE IN CHAIN C, LYS 45 TO ALA REMARK 400 ENGINEERED RESIDUE IN CHAIN C, LYS 47 TO ALA REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 N ALA C 47 O HOH C 2007 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 LEU A 218 CG LEU A 218 CD2 -0.285 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 LEU A 218 CB - CG - CD2 ANGL. DEV. = 10.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 230 32.52 75.15 REMARK 500 GLN B 285 57.35 -140.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 TYR A 223 ASN A 224 -144.25 REMARK 500 ASN A 224 ASN A 225 -142.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1305 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 47 O REMARK 620 2 TYR A 302 OH 93.9 REMARK 620 3 HOH A2067 O 91.4 79.6 REMARK 620 4 ALA C 47 O 174.5 88.9 93.7 REMARK 620 5 TYR C 302 OH 82.6 120.6 159.2 91.9 REMARK 620 6 HOH C2054 O 96.8 159.4 82.6 82.0 78.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 1305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT C 1305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 1306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 1306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1307 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2XMS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN NDRG2 PROTEIN PROVIDES INSIGHT INTO ITS REMARK 900 ROLE AS A TUMOR SUPPRESSOR REMARK 900 RELATED ID: 2XMQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN NDRG2 PROTEIN PROVIDES INSIGHT INTO ITS REMARK 900 ROLE AS A TUMOR SUPPRESSOR REMARK 999 REMARK 999 SEQUENCE REMARK 999 MUTANT OF PDB ID 2XMQ DBREF 2XMR A 24 304 UNP Q9UN36 NDRG2_HUMAN 24 304 DBREF 2XMR B 24 304 UNP Q9UN36 NDRG2_HUMAN 24 304 DBREF 2XMR C 24 304 UNP Q9UN36 NDRG2_HUMAN 24 304 SEQADV 2XMR ALA A 45 UNP Q9UN36 LYS 45 ENGINEERED MUTATION SEQADV 2XMR ALA A 47 UNP Q9UN36 LYS 47 ENGINEERED MUTATION SEQADV 2XMR ALA B 45 UNP Q9UN36 LYS 45 ENGINEERED MUTATION SEQADV 2XMR ALA B 47 UNP Q9UN36 LYS 47 ENGINEERED MUTATION SEQADV 2XMR ALA C 45 UNP Q9UN36 LYS 45 ENGINEERED MUTATION SEQADV 2XMR ALA C 47 UNP Q9UN36 LYS 47 ENGINEERED MUTATION SEQRES 1 A 281 ALA LYS THR HIS SER VAL GLU THR PRO TYR GLY SER VAL SEQRES 2 A 281 THR PHE THR VAL TYR GLY THR PRO ALA PRO ALA ARG PRO SEQRES 3 A 281 ALA ILE LEU THR TYR HIS ASP VAL GLY LEU ASN TYR LYS SEQRES 4 A 281 SER CYS PHE GLN PRO LEU PHE GLN PHE GLU ASP MET GLN SEQRES 5 A 281 GLU ILE ILE GLN ASN PHE VAL ARG VAL HIS VAL ASP ALA SEQRES 6 A 281 PRO GLY MET GLU GLU GLY ALA PRO VAL PHE PRO LEU GLY SEQRES 7 A 281 TYR GLN TYR PRO SER LEU ASP GLN LEU ALA ASP MET ILE SEQRES 8 A 281 PRO CYS VAL LEU GLN TYR LEU ASN PHE SER THR ILE ILE SEQRES 9 A 281 GLY VAL GLY VAL GLY ALA GLY ALA TYR ILE LEU ALA ARG SEQRES 10 A 281 TYR ALA LEU ASN HIS PRO ASP THR VAL GLU GLY LEU VAL SEQRES 11 A 281 LEU ILE ASN ILE ASP PRO ASN ALA LYS GLY TRP MET ASP SEQRES 12 A 281 TRP ALA ALA HIS LYS LEU THR GLY LEU THR SER SER ILE SEQRES 13 A 281 PRO GLU MET ILE LEU GLY HIS LEU PHE SER GLN GLU GLU SEQRES 14 A 281 LEU SER GLY ASN SER GLU LEU ILE GLN LYS TYR ARG ASN SEQRES 15 A 281 ILE ILE THR HIS ALA PRO ASN LEU ASP ASN ILE GLU LEU SEQRES 16 A 281 TYR TRP ASN SER TYR ASN ASN ARG ARG ASP LEU ASN PHE SEQRES 17 A 281 GLU ARG GLY GLY ASP ILE THR LEU ARG CYS PRO VAL MET SEQRES 18 A 281 LEU VAL VAL GLY ASP GLN ALA PRO HIS GLU ASP ALA VAL SEQRES 19 A 281 VAL GLU CYS ASN SER LYS LEU ASP PRO THR GLN THR SER SEQRES 20 A 281 PHE LEU LYS MET ALA ASP SER GLY GLY GLN PRO GLN LEU SEQRES 21 A 281 THR GLN PRO GLY LYS LEU THR GLU ALA PHE LYS TYR PHE SEQRES 22 A 281 LEU GLN GLY MET GLY TYR MET ALA SEQRES 1 B 281 ALA LYS THR HIS SER VAL GLU THR PRO TYR GLY SER VAL SEQRES 2 B 281 THR PHE THR VAL TYR GLY THR PRO ALA PRO ALA ARG PRO SEQRES 3 B 281 ALA ILE LEU THR TYR HIS ASP VAL GLY LEU ASN TYR LYS SEQRES 4 B 281 SER CYS PHE GLN PRO LEU PHE GLN PHE GLU ASP MET GLN SEQRES 5 B 281 GLU ILE ILE GLN ASN PHE VAL ARG VAL HIS VAL ASP ALA SEQRES 6 B 281 PRO GLY MET GLU GLU GLY ALA PRO VAL PHE PRO LEU GLY SEQRES 7 B 281 TYR GLN TYR PRO SER LEU ASP GLN LEU ALA ASP MET ILE SEQRES 8 B 281 PRO CYS VAL LEU GLN TYR LEU ASN PHE SER THR ILE ILE SEQRES 9 B 281 GLY VAL GLY VAL GLY ALA GLY ALA TYR ILE LEU ALA ARG SEQRES 10 B 281 TYR ALA LEU ASN HIS PRO ASP THR VAL GLU GLY LEU VAL SEQRES 11 B 281 LEU ILE ASN ILE ASP PRO ASN ALA LYS GLY TRP MET ASP SEQRES 12 B 281 TRP ALA ALA HIS LYS LEU THR GLY LEU THR SER SER ILE SEQRES 13 B 281 PRO GLU MET ILE LEU GLY HIS LEU PHE SER GLN GLU GLU SEQRES 14 B 281 LEU SER GLY ASN SER GLU LEU ILE GLN LYS TYR ARG ASN SEQRES 15 B 281 ILE ILE THR HIS ALA PRO ASN LEU ASP ASN ILE GLU LEU SEQRES 16 B 281 TYR TRP ASN SER TYR ASN ASN ARG ARG ASP LEU ASN PHE SEQRES 17 B 281 GLU ARG GLY GLY ASP ILE THR LEU ARG CYS PRO VAL MET SEQRES 18 B 281 LEU VAL VAL GLY ASP GLN ALA PRO HIS GLU ASP ALA VAL SEQRES 19 B 281 VAL GLU CYS ASN SER LYS LEU ASP PRO THR GLN THR SER SEQRES 20 B 281 PHE LEU LYS MET ALA ASP SER GLY GLY GLN PRO GLN LEU SEQRES 21 B 281 THR GLN PRO GLY LYS LEU THR GLU ALA PHE LYS TYR PHE SEQRES 22 B 281 LEU GLN GLY MET GLY TYR MET ALA SEQRES 1 C 281 ALA LYS THR HIS SER VAL GLU THR PRO TYR GLY SER VAL SEQRES 2 C 281 THR PHE THR VAL TYR GLY THR PRO ALA PRO ALA ARG PRO SEQRES 3 C 281 ALA ILE LEU THR TYR HIS ASP VAL GLY LEU ASN TYR LYS SEQRES 4 C 281 SER CYS PHE GLN PRO LEU PHE GLN PHE GLU ASP MET GLN SEQRES 5 C 281 GLU ILE ILE GLN ASN PHE VAL ARG VAL HIS VAL ASP ALA SEQRES 6 C 281 PRO GLY MET GLU GLU GLY ALA PRO VAL PHE PRO LEU GLY SEQRES 7 C 281 TYR GLN TYR PRO SER LEU ASP GLN LEU ALA ASP MET ILE SEQRES 8 C 281 PRO CYS VAL LEU GLN TYR LEU ASN PHE SER THR ILE ILE SEQRES 9 C 281 GLY VAL GLY VAL GLY ALA GLY ALA TYR ILE LEU ALA ARG SEQRES 10 C 281 TYR ALA LEU ASN HIS PRO ASP THR VAL GLU GLY LEU VAL SEQRES 11 C 281 LEU ILE ASN ILE ASP PRO ASN ALA LYS GLY TRP MET ASP SEQRES 12 C 281 TRP ALA ALA HIS LYS LEU THR GLY LEU THR SER SER ILE SEQRES 13 C 281 PRO GLU MET ILE LEU GLY HIS LEU PHE SER GLN GLU GLU SEQRES 14 C 281 LEU SER GLY ASN SER GLU LEU ILE GLN LYS TYR ARG ASN SEQRES 15 C 281 ILE ILE THR HIS ALA PRO ASN LEU ASP ASN ILE GLU LEU SEQRES 16 C 281 TYR TRP ASN SER TYR ASN ASN ARG ARG ASP LEU ASN PHE SEQRES 17 C 281 GLU ARG GLY GLY ASP ILE THR LEU ARG CYS PRO VAL MET SEQRES 18 C 281 LEU VAL VAL GLY ASP GLN ALA PRO HIS GLU ASP ALA VAL SEQRES 19 C 281 VAL GLU CYS ASN SER LYS LEU ASP PRO THR GLN THR SER SEQRES 20 C 281 PHE LEU LYS MET ALA ASP SER GLY GLY GLN PRO GLN LEU SEQRES 21 C 281 THR GLN PRO GLY LYS LEU THR GLU ALA PHE LYS TYR PHE SEQRES 22 C 281 LEU GLN GLY MET GLY TYR MET ALA HET CA A1305 1 HET ACT A1306 4 HET GOL A1307 6 HET ACT B1305 4 HET GOL B1306 6 HET ACT C1305 4 HET GOL C1306 6 HETNAM CA CALCIUM ION HETNAM ACT ACETATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 CA CA 2+ FORMUL 5 ACT 3(C2 H3 O2 1-) FORMUL 6 GOL 3(C3 H8 O3) FORMUL 11 HOH *399(H2 O) HELIX 1 1 ASN A 60 PHE A 65 1 6 HELIX 2 2 PHE A 65 PHE A 71 1 7 HELIX 3 3 PHE A 71 GLN A 79 1 9 HELIX 4 4 SER A 106 ASP A 112 1 7 HELIX 5 5 MET A 113 ASN A 122 1 10 HELIX 6 6 GLY A 132 HIS A 145 1 14 HELIX 7 7 GLY A 163 GLY A 174 1 12 HELIX 8 8 SER A 178 PHE A 188 1 11 HELIX 9 9 SER A 189 ASN A 196 1 8 HELIX 10 10 SER A 197 HIS A 209 1 13 HELIX 11 11 ASN A 212 ASN A 225 1 14 HELIX 12 12 HIS A 253 SER A 262 1 10 HELIX 13 13 GLN A 280 GLN A 285 1 6 HELIX 14 14 GLN A 285 GLY A 301 1 17 HELIX 15 15 ASN B 60 PHE B 65 1 6 HELIX 16 16 PHE B 65 PHE B 71 1 7 HELIX 17 17 PHE B 71 GLN B 79 1 9 HELIX 18 18 SER B 106 ASP B 112 1 7 HELIX 19 19 MET B 113 ASN B 122 1 10 HELIX 20 20 GLY B 132 HIS B 145 1 14 HELIX 21 21 GLY B 163 GLY B 174 1 12 HELIX 22 22 SER B 178 PHE B 188 1 11 HELIX 23 23 SER B 189 ASN B 196 1 8 HELIX 24 24 SER B 197 HIS B 209 1 13 HELIX 25 25 ASN B 212 ASN B 225 1 14 HELIX 26 26 HIS B 253 LEU B 264 1 12 HELIX 27 27 GLN B 280 GLN B 285 1 6 HELIX 28 28 GLN B 285 MET B 300 1 16 HELIX 29 29 ASN C 60 PHE C 65 1 6 HELIX 30 30 PHE C 65 GLN C 70 1 6 HELIX 31 31 PHE C 71 GLN C 79 1 9 HELIX 32 32 SER C 106 ASP C 112 1 7 HELIX 33 33 MET C 113 ASN C 122 1 10 HELIX 34 34 GLY C 132 HIS C 145 1 14 HELIX 35 35 GLY C 163 GLY C 174 1 12 HELIX 36 36 SER C 178 PHE C 188 1 11 HELIX 37 37 SER C 189 ASN C 196 1 8 HELIX 38 38 SER C 197 HIS C 209 1 13 HELIX 39 39 ASN C 212 ARG C 226 1 15 HELIX 40 40 HIS C 253 LEU C 264 1 12 HELIX 41 41 GLN C 280 GLN C 285 1 6 HELIX 42 42 GLN C 285 MET C 300 1 16 SHEET 1 AA 8 LYS A 25 THR A 31 0 SHEET 2 AA 8 GLY A 34 TYR A 41 -1 O GLY A 34 N THR A 31 SHEET 3 AA 8 ARG A 83 ASP A 87 -1 O ARG A 83 N TYR A 41 SHEET 4 AA 8 ALA A 50 TYR A 54 1 O ILE A 51 N VAL A 84 SHEET 5 AA 8 ILE A 126 VAL A 131 1 O ILE A 127 N LEU A 52 SHEET 6 AA 8 VAL A 149 ILE A 155 1 N GLU A 150 O ILE A 126 SHEET 7 AA 8 VAL A 243 GLY A 248 1 O MET A 244 N LEU A 154 SHEET 8 AA 8 THR A 269 MET A 274 1 O SER A 270 N LEU A 245 SHEET 1 BA 8 LYS B 25 THR B 31 0 SHEET 2 BA 8 GLY B 34 TYR B 41 -1 O GLY B 34 N THR B 31 SHEET 3 BA 8 ARG B 83 ASP B 87 -1 O ARG B 83 N TYR B 41 SHEET 4 BA 8 ALA B 50 TYR B 54 1 O ILE B 51 N VAL B 84 SHEET 5 BA 8 ILE B 126 VAL B 131 1 O ILE B 127 N LEU B 52 SHEET 6 BA 8 VAL B 149 ILE B 155 1 N GLU B 150 O ILE B 126 SHEET 7 BA 8 VAL B 243 GLY B 248 1 O MET B 244 N LEU B 154 SHEET 8 BA 8 THR B 269 MET B 274 1 O SER B 270 N LEU B 245 SHEET 1 CA 8 LYS C 25 THR C 31 0 SHEET 2 CA 8 GLY C 34 TYR C 41 -1 O GLY C 34 N THR C 31 SHEET 3 CA 8 ARG C 83 ASP C 87 -1 O ARG C 83 N TYR C 41 SHEET 4 CA 8 ALA C 50 TYR C 54 1 O ILE C 51 N VAL C 84 SHEET 5 CA 8 ILE C 126 VAL C 131 1 O ILE C 127 N LEU C 52 SHEET 6 CA 8 VAL C 149 ILE C 155 1 N GLU C 150 O ILE C 126 SHEET 7 CA 8 VAL C 243 GLY C 248 1 O MET C 244 N LEU C 154 SHEET 8 CA 8 THR C 269 MET C 274 1 O SER C 270 N LEU C 245 LINK O ALA A 47 CA CA A1305 1555 1555 2.65 LINK OH TYR A 302 CA CA A1305 1555 1555 2.85 LINK CA CA A1305 O HOH A2067 1555 1555 2.79 LINK CA CA A1305 O ALA C 47 1555 3554 2.77 LINK CA CA A1305 OH TYR C 302 1555 3554 2.95 LINK CA CA A1305 O HOH C2054 1555 3554 2.85 SITE 1 AC1 6 ALA A 47 TYR A 302 HOH A2067 ALA C 47 SITE 2 AC1 6 TYR C 302 HOH C2054 SITE 1 AC2 5 TYR B 41 TYR B 61 GLN B 75 ARG B 83 SITE 2 AC2 5 HIS B 85 SITE 1 AC3 7 TYR C 41 TYR C 61 PHE C 69 GLN C 75 SITE 2 AC3 7 ARG C 83 HIS C 85 HOH C2115 SITE 1 AC4 6 TYR A 61 GLN A 75 ILE A 78 ARG A 83 SITE 2 AC4 6 HIS A 85 HOH A2132 SITE 1 AC5 7 GLY B 58 LEU B 59 ASN B 60 SER B 63 SITE 2 AC5 7 MET B 91 ILE B 206 ASN B 212 SITE 1 AC6 8 GLY C 58 LEU C 59 ASN C 60 SER C 63 SITE 2 AC6 8 MET C 91 ILE C 206 ALA C 210 ASN C 212 SITE 1 AC7 8 GLY A 58 LEU A 59 ASN A 60 SER A 63 SITE 2 AC7 8 MET A 91 ILE A 206 ALA A 210 ASN A 212 CRYST1 86.232 88.049 126.907 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 0.011597 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011357 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007880 0.00000