HEADER SIGNALING PROTEIN 16-JUL-07 2QMQ TITLE CRYSTAL STRUCTURE OF A N-MYC DOWNSTREAM REGULATED 2 PROTEIN (NDRG2, TITLE 2 SYLD, NDR2, AI182517, AU040374) FROM MUS MUSCULUS AT 1.70 A TITLE 3 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN NDRG2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 40-313; COMPND 5 SYNONYM: PROTEIN NDR2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: 15277975, NDRG2, KIAA1248, NDR2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: HK100; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: SPEEDET KEYWDS ALPHA/BETA-HYDROLASES FOLD, NDR FAMILY, DEVELOPMENTAL PROTEIN, KEYWDS 2 DIFFERENTIATION, NEUROGENESIS, PHOSPHORYLATION, REGULATORY PROTEIN, KEYWDS 3 STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, KEYWDS 4 PROTEIN STRUCTURE INITIATIVE, PSI-2, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 8 20-SEP-23 2QMQ 1 REMARK REVDAT 7 25-JAN-23 2QMQ 1 REMARK SEQADV LINK REVDAT 6 24-JUL-19 2QMQ 1 REMARK REVDAT 5 25-OCT-17 2QMQ 1 REMARK REVDAT 4 15-JUN-11 2QMQ 1 JRNL REVDAT 3 23-MAR-11 2QMQ 1 TITLE KEYWDS REVDAT 2 24-FEB-09 2QMQ 1 VERSN REVDAT 1 04-SEP-07 2QMQ 0 JRNL AUTH J.HWANG,Y.KIM,H.B.KANG,L.JAROSZEWSKI,A.M.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 THE HUMAN N-MYC DOWNSTREAM-REGULATED JRNL TITL 2 GENE 2 PROTEIN PROVIDES INSIGHT INTO ITS ROLE AS A TUMOR JRNL TITL 3 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. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.35 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 28649 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) : 0.147 REMARK 3 R VALUE (WORKING SET) : 0.145 REMARK 3 FREE R VALUE : 0.183 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1449 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1302 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.1890 REMARK 3 BIN FREE R VALUE SET COUNT : 69 REMARK 3 BIN FREE R VALUE : 0.2430 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2152 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 27 REMARK 3 SOLVENT ATOMS : 314 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.36 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.35000 REMARK 3 B22 (A**2) : 0.35000 REMARK 3 B33 (A**2) : -0.53000 REMARK 3 B12 (A**2) : 0.18000 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): 0.098 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.097 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.059 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.438 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2304 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1525 ; 0.008 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3151 ; 1.561 ; 1.968 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3758 ; 0.953 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 301 ; 6.579 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 104 ;32.568 ;25.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 363 ;11.741 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;21.224 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 346 ; 0.094 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2603 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 445 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 469 ; 0.223 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1583 ; 0.193 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1128 ; 0.188 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1160 ; 0.087 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 223 ; 0.165 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.047 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 13 ; 0.150 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 40 ; 0.254 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 31 ; 0.169 ; 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): 1522 ; 1.454 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 572 ; 0.402 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2313 ; 1.977 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 964 ; 2.751 ; 4.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 826 ; 3.742 ; 5.000 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 : 1 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 -2 A 313 REMARK 3 ORIGIN FOR THE GROUP (A): 3.7832 34.5458 16.8449 REMARK 3 T TENSOR REMARK 3 T11: -0.0432 T22: -0.0141 REMARK 3 T33: -0.0311 T12: -0.0243 REMARK 3 T13: -0.0040 T23: 0.0002 REMARK 3 L TENSOR REMARK 3 L11: 0.7468 L22: 0.5567 REMARK 3 L33: 0.6603 L12: 0.2506 REMARK 3 L13: 0.1012 L23: 0.1081 REMARK 3 S TENSOR REMARK 3 S11: 0.0130 S12: -0.1019 S13: -0.0032 REMARK 3 S21: 0.0357 S22: -0.0449 S23: -0.0177 REMARK 3 S31: 0.0360 S32: 0.0075 S33: 0.0319 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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: 1. HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS REMARK 3 ONLY. 3. MG AND PEG 400 (2PE) ARE PRESENT IN THE CRYSTALLIZATION REMARK 3 CONDITIONS. 4. THE BENZOIC ACID (BEZ) MOLECULE IS ASSIGNED BASED REMARK 3 ON THE ELECTRON DENSITY AND ITS INTERACTION WITH THE PROTEIN. IT REMARK 3 COULD BE SOME RELATED COMPOUND WITH A SIMILAR STRUCTURE. REMARK 4 REMARK 4 2QMQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JUL-07. REMARK 100 THE DEPOSITION ID IS D_1000043792. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-OCT-05 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.019976 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28650 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 29.348 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.9 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : 0.05000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 61.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.40500 REMARK 200 R SYM FOR SHELL (I) : 0.40500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.900 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 1U2E REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NANODROP, 20.0% PEG 400, 0.2M MGCL2, REMARK 280 0.1M HEPES PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 277K, PH 7.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 71.58300 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 143.16600 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 143.16600 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 71.58300 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND 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 300 SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT REMARK 300 SCATTERING SUPPORTS THE ASSIGNMENT OF A MONOMER AS A REMARK 300 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE. 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 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 MET A -11 REMARK 465 GLY A -10 REMARK 465 SER A -9 REMARK 465 ASP A -8 REMARK 465 LYS A -7 REMARK 465 ILE A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -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 HIS A -3 CG ND1 CD2 CE1 NE2 REMARK 470 HIS A -2 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 61 CB CG CD CE NZ REMARK 470 TRP A 178 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 178 CZ3 CH2 REMARK 470 GLU A 212 CG CD OE1 OE2 REMARK 470 ARG A 247 CZ NH1 NH2 REMARK 470 GLU A 250 CD OE1 OE2 REMARK 470 LYS A 254 CD CE NZ REMARK 470 GLU A 305 CD OE1 OE2 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 O HOH A 520 O HOH A 527 2.05 REMARK 500 O HOH A 557 O HOH A 578 2.17 REMARK 500 O HOH A 465 O HOH A 519 2.17 REMARK 500 OE1 GLU A 107 O HOH A 535 2.18 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 210 45.48 36.72 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 LYS A 61 ARG A 62 -134.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 2PE A 4 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 MG A 1 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 344 O REMARK 620 2 HOH A 358 O 171.7 REMARK 620 3 HOH A 377 O 89.1 92.0 REMARK 620 4 HOH A 385 O 87.3 92.0 175.0 REMARK 620 5 HOH A 392 O 90.1 81.8 85.2 98.2 REMARK 620 6 HOH A 397 O 86.9 101.3 85.3 91.1 170.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 2 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 244 OD1 REMARK 620 2 HOH A 418 O 84.9 REMARK 620 3 HOH A 421 O 92.6 88.5 REMARK 620 4 HOH A 429 O 178.5 94.7 88.8 REMARK 620 5 HOH A 441 O 92.7 80.0 166.8 85.8 REMARK 620 6 HOH A 486 O 86.9 171.7 93.0 93.4 99.3 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 MG A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BEZ A 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2PE A 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 358981 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE CONSTRUCT CONSISTS OF RESIDUES 40-313 OF THE REMARK 999 FULL LENGTH PROTEIN. IT WAS EXPRESSED WITH A REMARK 999 PURIFICATION TAG MGSDKIHHHHHH. DBREF 2QMQ A 40 313 UNP Q9QYG0 NDRG2_MOUSE 40 313 SEQADV 2QMQ MET A -11 UNP Q9QYG0 EXPRESSION TAG SEQADV 2QMQ GLY A -10 UNP Q9QYG0 EXPRESSION TAG SEQADV 2QMQ SER A -9 UNP Q9QYG0 EXPRESSION TAG SEQADV 2QMQ ASP A -8 UNP Q9QYG0 EXPRESSION TAG SEQADV 2QMQ LYS A -7 UNP Q9QYG0 EXPRESSION TAG SEQADV 2QMQ ILE A -6 UNP Q9QYG0 EXPRESSION TAG SEQADV 2QMQ HIS A -5 UNP Q9QYG0 EXPRESSION TAG SEQADV 2QMQ HIS A -4 UNP Q9QYG0 EXPRESSION TAG SEQADV 2QMQ HIS A -3 UNP Q9QYG0 EXPRESSION TAG SEQADV 2QMQ HIS A -2 UNP Q9QYG0 EXPRESSION TAG SEQADV 2QMQ HIS A -1 UNP Q9QYG0 EXPRESSION TAG SEQADV 2QMQ HIS A 0 UNP Q9QYG0 EXPRESSION TAG SEQRES 1 A 286 MET GLY SER ASP LYS ILE HIS HIS HIS HIS HIS HIS THR SEQRES 2 A 286 HIS SER VAL GLU THR PRO TYR GLY SER VAL THR PHE THR SEQRES 3 A 286 VAL TYR GLY THR PRO LYS PRO LYS ARG PRO ALA ILE PHE SEQRES 4 A 286 THR TYR HIS ASP VAL GLY LEU ASN TYR LYS SER CYS PHE SEQRES 5 A 286 GLN PRO LEU PHE ARG PHE GLY ASP MET GLN GLU ILE ILE SEQRES 6 A 286 GLN ASN PHE VAL ARG VAL HIS VAL ASP ALA PRO GLY MET SEQRES 7 A 286 GLU GLU GLY ALA PRO VAL PHE PRO LEU GLY TYR GLN TYR SEQRES 8 A 286 PRO SER LEU ASP GLN LEU ALA ASP MET ILE PRO CYS ILE SEQRES 9 A 286 LEU GLN TYR LEU ASN PHE SER THR ILE ILE GLY VAL GLY SEQRES 10 A 286 VAL GLY ALA GLY ALA TYR ILE LEU SER ARG TYR ALA LEU SEQRES 11 A 286 ASN HIS PRO ASP THR VAL GLU GLY LEU VAL LEU ILE ASN SEQRES 12 A 286 ILE ASP PRO ASN ALA LYS GLY TRP MET ASP TRP ALA ALA SEQRES 13 A 286 HIS LYS LEU THR GLY LEU THR SER SER ILE PRO ASP MET SEQRES 14 A 286 ILE LEU GLY HIS LEU PHE SER GLN GLU GLU LEU SER GLY SEQRES 15 A 286 ASN SER GLU LEU ILE GLN LYS TYR ARG GLY ILE ILE GLN SEQRES 16 A 286 HIS ALA PRO ASN LEU GLU ASN ILE GLU LEU TYR TRP ASN SEQRES 17 A 286 SER TYR ASN ASN ARG ARG ASP LEU ASN PHE GLU ARG GLY SEQRES 18 A 286 GLY GLU THR THR LEU LYS CYS PRO VAL MET LEU VAL VAL SEQRES 19 A 286 GLY ASP GLN ALA PRO HIS GLU ASP ALA VAL VAL GLU CYS SEQRES 20 A 286 ASN SER LYS LEU ASP PRO THR GLN THR SER PHE LEU LYS SEQRES 21 A 286 MET ALA ASP SER GLY GLY GLN PRO GLN LEU THR GLN PRO SEQRES 22 A 286 GLY LYS LEU THR GLU ALA PHE LYS TYR PHE LEU GLN GLY HET MG A 1 1 HET MG A 2 1 HET BEZ A 3 9 HET 2PE A 4 16 HETNAM MG MAGNESIUM ION HETNAM BEZ BENZOIC ACID HETNAM 2PE NONAETHYLENE GLYCOL FORMUL 2 MG 2(MG 2+) FORMUL 4 BEZ C7 H6 O2 FORMUL 5 2PE C18 H38 O10 FORMUL 6 HOH *314(H2 O) HELIX 1 1 ASN A 74 ARG A 84 1 11 HELIX 2 2 PHE A 85 GLN A 93 1 9 HELIX 3 3 SER A 120 MET A 127 1 8 HELIX 4 4 MET A 127 ASN A 136 1 10 HELIX 5 5 GLY A 146 HIS A 159 1 14 HELIX 6 6 GLY A 177 LEU A 189 1 13 HELIX 7 7 SER A 192 PHE A 202 1 11 HELIX 8 8 SER A 203 GLY A 209 1 7 HELIX 9 9 SER A 211 HIS A 223 1 13 HELIX 10 10 ASN A 226 ASN A 239 1 14 HELIX 11 11 HIS A 267 LEU A 278 1 12 HELIX 12 12 ASP A 279 THR A 281 5 3 HELIX 13 13 GLN A 294 GLN A 299 1 6 HELIX 14 14 GLN A 299 GLN A 312 1 14 SHEET 1 A 8 HIS A -2 THR A 45 0 SHEET 2 A 8 GLY A 48 TYR A 55 -1 O VAL A 54 N HIS A -1 SHEET 3 A 8 ARG A 97 ASP A 101 -1 O ASP A 101 N THR A 51 SHEET 4 A 8 ALA A 64 TYR A 68 1 N ILE A 65 O VAL A 98 SHEET 5 A 8 ILE A 140 VAL A 145 1 O ILE A 141 N PHE A 66 SHEET 6 A 8 VAL A 163 ILE A 169 1 O VAL A 167 N GLY A 142 SHEET 7 A 8 VAL A 257 GLY A 262 1 O MET A 258 N LEU A 166 SHEET 8 A 8 THR A 283 MET A 288 1 O SER A 284 N LEU A 259 SHEET 1 B 2 GLU A 246 ARG A 247 0 SHEET 2 B 2 GLU A 250 THR A 251 -1 O GLU A 250 N ARG A 247 LINK MG MG A 1 O HOH A 344 1555 1555 2.07 LINK MG MG A 1 O HOH A 358 1555 1555 2.08 LINK MG MG A 1 O HOH A 377 1555 1555 2.01 LINK MG MG A 1 O HOH A 385 1555 1555 2.04 LINK MG MG A 1 O HOH A 392 1555 1555 2.16 LINK MG MG A 1 O HOH A 397 1555 1555 1.94 LINK MG MG A 2 OD1 ASN A 244 1555 1555 2.10 LINK MG MG A 2 O HOH A 418 1555 1555 2.08 LINK MG MG A 2 O HOH A 421 1555 1555 2.27 LINK MG MG A 2 O HOH A 429 1555 1555 2.17 LINK MG MG A 2 O HOH A 441 1555 1555 2.08 LINK MG MG A 2 O HOH A 486 1555 1555 2.13 SITE 1 AC1 6 HOH A 344 HOH A 358 HOH A 377 HOH A 385 SITE 2 AC1 6 HOH A 392 HOH A 397 SITE 1 AC2 6 ASN A 244 HOH A 418 HOH A 421 HOH A 429 SITE 2 AC2 6 HOH A 441 HOH A 486 SITE 1 AC3 8 TYR A 55 TYR A 75 GLN A 80 PHE A 83 SITE 2 AC3 8 ARG A 84 ARG A 97 HIS A 99 HOH A 424 SITE 1 AC4 10 LEU A 132 GLN A 133 ASN A 136 PHE A 137 SITE 2 AC4 10 TYR A 155 HIS A 159 HIS A 223 HOH A 540 SITE 3 AC4 10 HOH A 579 HOH A 627 CRYST1 46.371 46.371 214.749 90.00 90.00 120.00 P 31 2 1 6 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.021565 0.012451 0.000000 0.00000 SCALE2 0.000000 0.024901 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004657 0.00000